From a778a70ba84ce53ffe189038642b3f2aec9ffe77 Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 30 Oct 2021 16:51:40 +0200
Subject: [PATCH 1/4] add gitignore additions

---
 .gitignore | 69 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 69 insertions(+)

diff --git a/.gitignore b/.gitignore
index 9e75cc10f6..c57db22f85 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,71 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+*.7z
+*.dmg
+#*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+#*.bz
+.hg
+*.swp
+.DS_Store
+
+# Tool test from planemo
 tool_test_output.html
 tool_test_output.json
+
+# Tool test from galaxy-language-server
+*_test_report.html

From 6dd3e529c9f97269a5b60c2569ec90cc43a9077c Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 30 Oct 2021 16:53:05 +0200
Subject: [PATCH 2/4] changes to camera

---
 .../abims_CAMERA_annotateDiffreport.xml       | 224 +++++-------------
 .../repository_dependencies.xml               |   1 -
 .../abims_CAMERA_combinexsAnnos.xml           | 122 +++-------
 .../repository_dependencies.xml               |   1 -
 tools/camera_macro/macros.xml                 |  99 +++-----
 .../camera_macro/repository_dependencies.xml  |   5 -
 .../repository_dependencies.xml               |   6 -
 7 files changed, 126 insertions(+), 332 deletions(-)
 delete mode 120000 tools/camera_annotate/repository_dependencies.xml
 delete mode 120000 tools/camera_combinexsannos/repository_dependencies.xml
 delete mode 100644 tools/camera_macro/repository_dependencies.xml
 delete mode 100644 tools/camera_repository_suite/repository_dependencies.xml

diff --git a/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml b/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
index c400c83993..c962b5f330 100644
--- a/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
+++ b/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
@@ -1,16 +1,12 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.6+camera@TOOL_VERSION@-galaxy0">
-
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.6+camera@TOOL_VERSION@-galaxy0" profile="21.09">
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
-
     <macros>
         <import>macros.xml</import>
     </macros>
-
     <expand macro="requirements"/>
     <expand macro="stdio"/>
-
     <command><![CDATA[
-        @COMMAND_RSCRIPT@/CAMERA_annotateDiffreport.r
+        LC_ALL=C Rscript '$__tool_directory__/CAMERA_annotateDiffreport.r'
         image '$image'
 
         nSlaves \${GALAXY_SLOTS:-1}
@@ -44,7 +40,7 @@
             #if $quick_block.findadducts.rules_block.rules_select == "FALSE":
                 multiplier $quick_block.findadducts.rules_block.multiplier
             #else
-                rules $quick_block.findadducts.rules_block.rules
+                rules '$quick_block.findadducts.rules_block.rules'
             #end if
         #end if
 
@@ -67,92 +63,85 @@
         @COMMAND_FILE_LOAD@
 
     ]]></command>
-
+    <required_files>
+        <include path="lib.r" />
+        <include path="CAMERA_annotateDiffreport.r" />
+    </required_files>
     <inputs>
-
-
-        <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />
-
-        <section name="groupfwhm" title="Group co-eluted peaks based on RT [groupFWHM]"  expanded="True">
-            <param name="sigma" type="integer" value="6" label="Multiplier of the standard deviation" help="[sigma]" />
-            <param name="perfwhm" type="float" value="0.6" max="1" min="0" label="Percentage of FWHM width" help="[perfwhm]" />
+        <param name="image" type="data" format="rdata.xcms.fillpeaks,rdata" label="RData file" help="Output file from xcms fillPeaks"/>
+        <section name="groupfwhm" title="Group co-eluted peaks based on RT [groupFWHM]" expanded="True">
+            <param argument="sigma" type="integer" value="6" label="Multiplier of the standard deviation"/>
+            <param argument="perfwhm" type="float" value="0.6" max="1" min="0" label="Percentage of FWHM width"/>
         </section>
-
-        <section name="findgeneral" title="Annotation general options"  expanded="True">
-            <param name="ppm" type="integer" value="5" label="General ppm error" help="[ppm]" />
-            <param name="mzabs" type="float" value="0.015" label="General absolut error in m/z" help="[mzabs]" />
+        <section name="findgeneral" title="Annotation general options" expanded="True">
+            <param argument="ppm" type="integer" value="5" label="General ppm error"/>
+            <param argument="mzabs" type="float" value="0.015" label="General absolut error in m/z"/>
         </section>
-
-        <section name="findisotopes" title="Annotate Isotopes [findIsotopes]"  expanded="True">
-            <param name="maxcharge" type="integer" value="3" label="Max. ion charge" help="[maxcharge]" />
-            <param name="maxiso" type="integer" value="4" label="Max. number of expected isotopes" help="[maxiso]" />
-            <param name="minfrac" type="float" value="0.5" max="1" min="0" label="The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation" help="[minfrac]" />
+        <section name="findisotopes" title="Annotate Isotopes [findIsotopes]" expanded="True">
+            <param argument="maxcharge" type="integer" value="3" label="Max. ion charge"/>
+            <param argument="maxiso" type="integer" value="4" label="Max. number of expected isotopes" help=""/>
+            <param argument="minfrac" type="float" value="0.5" max="1" min="0" label="The percentage number of samples, which must satisfy the C12/C13 rule for isotope annotation"/>
         </section>
-
         <conditional name="quick_block">
-            <param name="quick" type="select" label="Mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts">
+            <param argument="quick" type="select" label="Mode" help="[quick] If TRUE, use only groupFWHM and findIsotopes functions. Else if FALSE, use also groupCorr and findAdducts">
                 <option value="FALSE" selected="true">All functions</option>
-                <option value="TRUE">Only groupFWHM and findIsotopes functions [quick]</option>
+                <option value="TRUE">Only groupFWHM and findIsotopes functions (quick)</option>
             </param>
             <when value="FALSE">
-
-                <section name="groupcorr" title="Verifying grouping co-eluted peaks [groupCorr]"  expanded="True">
-                    <param name="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)" help="[cor_eic_th]" />
-                    <param name="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra" help="[graphMethod]">
+                <section name="groupcorr" title="Verifying grouping co-eluted peaks [groupCorr]" expanded="True">
+                    <param argument="cor_eic_th" type="float" value="0.75" max="1" min="0" label="groupCorr: correlation threshold (0..1)"/>
+                    <param argument="graphMethod" type="select" label="groupCorr: Method selection for grouping peaks after correlation analysis into pseudospectra">
                         <option value="hcs" selected="true">hcs</option>
                         <option value="lpc">lpc</option>
                     </param>
-                    <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" />
-                    <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/>
-                    <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/>
-                    <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/>
+                    <param argument="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold"/>
+                    <param argument="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping"/>
+                    <param argument="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping"/>
+                    <param argument="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping"/>
                 </section>
-
-                <section name="findadducts" title="Annotate Adducts [findAdducts]"  expanded="True">
-                    <param name="polarity" type="select" label="Which polarity mode was used for measuring of the ms sample" help="polarity">
-                        <option value="positive" >positive</option>
+                <section name="findadducts" title="Annotate Adducts [findAdducts]" expanded="True">
+                    <param argument="polarity" type="select" label="Which polarity mode was used for measuring of the ms sample">
+                        <option value="positive">positive</option>
                         <option value="negative" selected="true">negative</option>
                     </param>
-                    <param name="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode" help="[max_peaks]" />
+                    <param argument="max_peaks" type="integer" value="100" label="How much peaks will be calculated in every thread using the parallel mode"/>
                     <conditional name="rules_block">
                         <param name="rules_select" type="select" label="Use a personal ruleset file">
-                            <option value="TRUE">TRUE</option>
-                            <option value="FALSE" selected="true">FALSE</option>
+                            <option value="TRUE">Yes</option>
+                            <option value="FALSE" selected="true">No</option>
                         </param>
                         <when value="FALSE">
-                            <param name="multiplier" type="integer" value="3" label="If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" />
+                            <param argument="multiplier" type="integer" value="3" label="If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions"/>
                         </when>
                         <when value="TRUE">
-                            <param name="rules" type="data" format="csv" label="User defined ruleset" help="[rules]" />
+                            <param argument="rules" type="data" format="csv" label="User defined ruleset"/>
                         </when>
                     </conditional>
                 </section>
-
             </when>
             <when value="TRUE">
-                <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" />
+                <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label"/>
             </when>
         </conditional>
-
         <!-- Diffreport specific parameters -->
-        <section name="diffreport" title="Statistics and results export: [diffreport]"  expanded="True">
+        <section name="diffreport" title="Statistics and results export: [diffreport]" expanded="True">
             <conditional name="options">
                 <param name="option" type="select" label="Number of condition">
                     <option value="hide" selected="true">One condition</option>
                     <option value="show">Two or more conditions</option>
                 </param>
                 <when value="show">
-                    <param name="eicmax" type="integer" value="0" label="Number of the most significantly different analytes to create EICs for" help="[eicmax]" />
-                    <param name="eicwidth" type="integer" value="200" label="Width (in seconds) of EICs produced" help="[eicwidth]" />
-                    <param name="value" type="select" label="Intensity values to be used for the diffreport" help="[value]">
+                    <param argument="eicmax" type="integer" value="0" label="Number of the most significantly different analytes to create EICs for"/>
+                    <param argument="eicwidth" type="integer" value="200" label="Width (in seconds) of EICs produced"/>
+                    <param argument="value" type="select" label="Intensity values to be used for the diffreport">
                         <option value="into" selected="true">into</option>
-                        <option value="maxo" >maxo</option>
+                        <option value="maxo">maxo</option>
                         <option value="intb">intb</option>
                     </param>
-                    <param name="h" type="integer" value="480" label="Numeric variable for the height of the eic and boxplots that are printed out" help="[height]" />
-                    <param name="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made" help="[width]" />
-                    <param name="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot" help="[mzdec]" />
-                    <param name="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value" help="[sortpval]"/>
+                    <param argument="h" type="integer" value="480" label="Numeric variable for the height of the eic and boxplots that are printed out"/>
+                    <param argument="w" type="integer" value="640" label="Numeric variable for the width of the eic and boxplots print out made"/>
+                    <param argument="mzdec" type="integer" value="2" label="Number of decimal places of title m/z values in the eic plot"/>
+                    <param argument="sortpval" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="logical indicating whether the reports should be sorted by p-value"/>
                     <param name="tabular2" type="select" label="Export the Diffreport files in ">
                         <option value="zip" selected="true">Zip</option>
                         <option value="datasetcollection">Individual file in a Dataset Collection</option>
@@ -166,57 +155,52 @@
                 </when>
             </conditional>
         </section>
-
         <expand macro="input_peaklist"/>
         <expand macro="input_file_load"/>
     </inputs>
-
     <outputs>
-        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
-        <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata"  from_work_dir="annotatediff.RData">
+        <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.annotate.variableMetadata.tsv" from_work_dir="variableMetadata.tsv"/>
+        <data name="rdata_quick_false" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.${$quick_block.findadducts.polarity}.Rdata" from_work_dir="annotatediff.RData">
             <filter>quick_block['quick'] == 'FALSE'</filter>
             <change_format>
-                <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive" />
-                <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative" />
+                <when input="quick_block.findadducts.polarity" value="positive" format="rdata.camera.positive"/>
+                <when input="quick_block.findadducts.polarity" value="negative" format="rdata.camera.negative"/>
             </change_format>
         </data>
         <data name="rdata_quick_true" format="rdata.camera.quick" label="${image.name[:-6]}.annotate.quick.Rdata" from_work_dir="annotatediff.RData">
             <filter>quick_block['quick'] == 'TRUE'</filter>
         </data>
-
-        <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip" >
-            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'zip'</filter>
+        <data name="output_diffreport_eic_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_eic.zip" from_work_dir="eic.zip">
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] &gt; 0 and diffreport['options']['png2'] == 'zip'</filter>
         </data>
-        <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip" >
-            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'zip'</filter>
+        <data name="output_diffreport_box_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_box.zip" from_work_dir="box.zip">
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] &gt; 0 and diffreport['options']['png2'] == 'zip'</filter>
         </data>
         <collection name="output_diffreport_picture_pdf" type="list" label="${image.name[:-6]}.annotateDiffreport.pdf">
-            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] > 0 and diffreport['options']['png2'] == 'pdf'</filter>
-            <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf" />
+            <filter>diffreport['options']['option'] == 'show' and diffreport['options']['eicmax'] &gt; 0 and diffreport['options']['png2'] == 'pdf'</filter>
+            <discover_datasets pattern="__designation_and_ext__" directory="pdf" format="pdf"/>
         </collection>
-
         <data name="output_diffreport_table_zip" format="zip" label="${image.name[:-6]}.annotateDiffreport_table.zip" from_work_dir="tabular.zip">
             <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'zip'</filter>
         </data>
         <collection name="output_diffreport_table_collection" type="list" label="${image.name[:-6]}.annotateDiffreport_table">
             <filter>diffreport['options']['option'] == 'show' and diffreport['options']['tabular2'] == 'datasetcollection'</filter>
-            <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular" />
+            <discover_datasets pattern="__designation_and_ext__" directory="tabular" format="tabular"/>
         </collection>
     </outputs>
-
     <tests>
         <test>
             <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData"/>
             <expand macro="test_annotate_diffreport"/>
             <expand macro="test_annotate_quick_true"/>
             <expand macro="test_file_load_single"/>
-            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" lines_diff="2" />
+            <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" lines_diff="2"/>
         </test>
         <test>
             <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.fillpeaks.RData"/>
             <expand macro="test_annotate_diffreport"/>
             <conditional name="quick_block">
-                <expand macro="test_annotate_quick_false" />
+                <expand macro="test_annotate_quick_false"/>
                 <section name="findadducts">
                     <param name="polarity" value="negative"/>
                     <conditional name="rules_block">
@@ -229,9 +213,6 @@
             <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.rules.variableMetadata.tsv" lines_diff="2"/>
         </test>
     </tests>
-
-
-
     <help><![CDATA[
 
 @HELP_AUTHORS@
@@ -422,93 +403,6 @@ Changelog/News
 
 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
 
-@HELP_CAMERA_NEWVERSION_1480@
-
-@HELP_CAMERA_NEWVERSION_1460@
-
-**Version 2.2.6+camera1.42.0-galaxy1 - 09/03/2020**
-
-- BUGFIX: Fix the zip export of the pictures (eic and boxplot)
-
-@HELP_CAMERA_NEWVERSION_1420@
-
-**Version 2.2.5 - 09/04/2019**
-
-- NEW: zip export are back for pictures (eic and boxplot) and diffreport tables
-
-- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
-
-- UPGRADE: refactoring of internal code
-
-**Version 2.2.4 - 09/10/2018**
-
-- NEW: CAMERA.annotate no longer export a DataMatrix. fillChromPeaks does the job
-
-**Version 2.2.3 - 30/04/2018**
-
-- NEW: support the new xcms 3.0.0 wrapper
-
-**Version 2.2.2 - 01/03/2018**
-
-- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
-
-**Version 2.2.1 - 29/11/2017**
-
-- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
-
-**Version 2.2.0 - 28/03/2017**
-
-- BUGFIX: the diffreport ids didn't convert the rt in minute as the other export
-
-- UPDATE: the settings (digits, convertion in minutes) of the identifiants will no longer modify the native one. Because we want to be conservative and because it can be dangerous for the data integrity during a futur merge of the table, we decide to put those customization in a new column namecustom within the variableMetadata.
-
-- IMPROVEMENT: add some sections within to separate the different parts of the process
-
-- IMPROVEMENT: add the possibility to use defined ruleset
-
-- IMPROVEMENT: add the possibility to set the MZ digit within the identifiants
-
-- IMPROVEMENT: CAMERA.annotate is now compatible with merged individual data from xcms.xcmsSet
-
-
-**Version 2.1.5 - 21/04/2016**
-
-- UPGRADE: upgrade the CAMERA version from 1.22.0 to 1.26.0
-
-
-**Version 2.1.4 - 18/04/2016**
-
-- TEST: refactoring to pass planemo test using conda dependencies
-
-
-**Version 2.1.3 - 10/02/2016**
-
-- BUGFIX: better management of errors. Datasets remained green although the process failed
-
-- BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions)
-
-- IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf.
-
-- UPDATE: refactoring of internal management of inputs/outputs
-
-
-**VERSION 2.1.0 - 09/10/2015**
-
-- BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites))
-
-
-**VERSION 2.1.0 - 07/06/2015**
-
-- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
-
-- IMPROVEMENT: parameter labels have changed to facilitate their reading.
-
-- UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
-
-
     ]]></help>
-
-    <expand macro="citation" />
-
-
+    <expand macro="citation"/>
 </tool>
diff --git a/tools/camera_annotate/repository_dependencies.xml b/tools/camera_annotate/repository_dependencies.xml
deleted file mode 120000
index 2715c82a0c..0000000000
--- a/tools/camera_annotate/repository_dependencies.xml
+++ /dev/null
@@ -1 +0,0 @@
-../camera_macro/repository_dependencies.xml
\ No newline at end of file
diff --git a/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml b/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
index 8d0a1262d9..4c8d3087fe 100644
--- a/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
+++ b/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
@@ -1,57 +1,51 @@
-<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.6+camera@TOOL_VERSION@-galaxy0">
-
-    <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
-
+<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.6+camera@TOOL_VERSION@-galaxy0" profile="20.09">
+    <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-
     <expand macro="requirements"/>
     <expand macro="stdio"/>
-
     <command><![CDATA[
-        @COMMAND_RSCRIPT@/CAMERA_combinexsAnnos.r
+        LC_ALL=C Rscript '$__tool_directory__/CAMERA_combinexsAnnos.r'
         image_pos '$image_pos'
         image_neg '$image_neg'
 
-        pos $pos tol
-        $tol ruleset
-        $ruleset keep_meta
-        $keep_meta
+        pos $pos
+        tol $tol
+        ruleset '$ruleset'
+        keep_meta $keep_meta
 
         convertRTMinute $export.convertRTMinute
         numDigitsMZ $export.numDigitsMZ
         numDigitsRT $export.numDigitsRT
 
-    ]]></command>
-
+    ]]>    </command>
+    <required_files>
+        <include path="lib.r" />
+        <include path="CAMERA_combinexsAnnos.r" />
+    </required_files>
     <inputs>
-        <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
-        <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
-
-        <param name="pos" type="select" label="Returned peaklist polarity mode">
+        <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode"/>
+        <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode"/>
+        <param argument="pos" type="select" label="Returned peaklist polarity mode">
             <option value="TRUE" selected="true">positive</option>
-            <option value="FALSE" >negative</option>
+            <option value="FALSE">negative</option>
         </param>
-
-        <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" />
-        <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />
-        <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
-
+        <param argument="tol" type="integer" value="2" label="Retention time window in seconds" help="As first step it searches for pseudospectra from the positive and the negative sample within a retention time window"/>
+        <param argument="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!"/>
+        <param argument="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
         <section name="export" title="Export options">
-            <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
-            <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
-            <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
+            <param argument="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
+            <param argument="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers"/>
+            <param argument="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers"/>
         </section>
     </inputs>
-
     <outputs>
-        <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" from_work_dir="variableMetadata.tsv" />
+        <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" from_work_dir="variableMetadata.tsv"/>
         <!--
         <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" from_work_dir="combinexsAnnos.RData" />
         -->
     </outputs>
-
     <tests>
         <test>
             <!-- TODO: generer des vrais dataset pos et neg-->
@@ -62,14 +56,12 @@
             <param name="ruleset" value="1,1"/>
             <section name="export">
                 <param name="convertRTMinute" value="True"/>
-                <param name="numDigitsMZ" value="4" />
-                <param name="numDigitsRT" value="1" />
+                <param name="numDigitsMZ" value="4"/>
+                <param name="numDigitsRT" value="1"/>
             </section>
-            <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
+            <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv"/>
         </test>
     </tests>
-
-
     <help><![CDATA[
 
 @HELP_AUTHORS@
@@ -102,7 +94,6 @@ A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@r
 xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!
 
 
-
 -----------------
 Workflow position
 -----------------
@@ -211,63 +202,6 @@ Changelog/News
 
 .. _News: https://bioconductor.org/packages/release/bioc/news/CAMERA/NEWS
 
-@HELP_CAMERA_NEWVERSION_1480@
-
-@HELP_CAMERA_NEWVERSION_1460@
-
-@HELP_CAMERA_NEWVERSION_1420@
-
-**Version 2.2.5 - 09/04/2019**
-
-- UPGRADE: upgrade the CAMERA version from 1.34.0 to 1.38.1 (see CAMERA News_)
-
-- UPGRADE: refactoring of internal code
-
-**Version 2.2.2 - 01/03/2018**
-
-- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
-
-**Version 2.0.7 - 29/11/2017**
-
-- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
-
-
-**Version 2.0.6 - 10/02/2017**
-
-- IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate)
-
-
-**Version 2.0.5 - 22/12/2016**
-
-- IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset)
-
-**Version 2.0.4 - 21/04/2016**
-
-- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0
-
-
-**Version 2.0.3 - 10/02/2016**
-
-- BUGFIX: better management of errors. Datasets remained green although the process failed
-
-- UPDATE: refactoring of internal management of inputs/outputs
-
-
-**Version 2.0.1 - 07/06/2015**
-
-- IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
-
-- IMPROVEMENT: parameter labels have changed to facilitate their reading.
-
-
-**Version 2.0.0 - 09/06/2015**
-
-- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
-
-
-    ]]></help>
-
-    <expand macro="citation" />
-
-
+    ]]>    </help>
+    <expand macro="citation"/>
 </tool>
diff --git a/tools/camera_combinexsannos/repository_dependencies.xml b/tools/camera_combinexsannos/repository_dependencies.xml
deleted file mode 120000
index 2715c82a0c..0000000000
--- a/tools/camera_combinexsannos/repository_dependencies.xml
+++ /dev/null
@@ -1 +0,0 @@
-../camera_macro/repository_dependencies.xml
\ No newline at end of file
diff --git a/tools/camera_macro/macros.xml b/tools/camera_macro/macros.xml
index 8b4b6b481d..d8927f9cd4 100644
--- a/tools/camera_macro/macros.xml
+++ b/tools/camera_macro/macros.xml
@@ -1,6 +1,5 @@
 <?xml version="1.0"?>
 <macros>
-
     <token name="@TOOL_VERSION@">1.48.0</token>
     <xml name="requirements">
         <requirements>
@@ -19,8 +18,6 @@
         </stdio>
     </xml>
 
-    <token name="@COMMAND_RSCRIPT@">LC_ALL=C Rscript $__tool_directory__/</token>
-
     <!-- raw file load for planemo test -->
     <token name="@COMMAND_FILE_LOAD@">
         #if $file_load_section.file_load_conditional.file_load_select == "yes":
@@ -37,9 +34,9 @@
     <xml name="input_file_load">
         <section name="file_load_section" title="Resubmit your raw dataset or your zip file">
             <conditional name="file_load_conditional">
-                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." >
-                    <option value="no" >no need</option>
-                    <option value="yes" >yes</option>
+                <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server.">
+                    <option value="no">no need</option>
+                    <option value="yes">yes</option>
                 </param>
                 <when value="no">
                 </when>
@@ -78,12 +75,12 @@
 
     <xml name="input_peaklist">
         <section name="export" title="Export options">
-            <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
-            <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
-            <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
-            <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below">
+            <param argument="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes" />
+            <param argument="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
+            <param argument="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
+            <param argument="intval" type="select" label="General used intensity value" help="See the help section below">
                 <option value="into" selected="true">into</option>
-                <option value="maxo" >maxo</option>
+                <option value="maxo">maxo</option>
                 <option value="intb">intb</option>
             </param>
         </section>
@@ -91,61 +88,61 @@
 
     <xml name="test_peaklist">
         <section name="export">
-            <param name="convertRTMinute" value="True"/>
+            <param name="convertRTMinute" value="True" />
             <param name="numDigitsMZ" value="4" />
             <param name="numDigitsRT" value="1" />
-            <param name="intval" value="into"/>
+            <param name="intval" value="into" />
         </section>
     </xml>
 
     <!-- annotate_diffreport <test> commun part -->
     <xml name="test_annotate_diffreport">
         <section name="groupfwhm">
-            <param name="sigma" value="6"/>
-            <param name="perfwhm" value="0.6"/>
+            <param name="sigma" value="6" />
+            <param name="perfwhm" value="0.6" />
         </section>
         <section name="findisotopes">
-            <param name="maxcharge" value="3"/>
-            <param name="maxiso" value="4"/>
-            <param name="minfrac" value="0.5"/>
+            <param name="maxcharge" value="3" />
+            <param name="maxiso" value="4" />
+            <param name="minfrac" value="0.5" />
         </section>
         <section name="findgeneral">
-            <param name="ppm" value="5"/>
-            <param name="mzabs" value="0.015"/>
-            <param name="max_peaks" value="100"/>
+            <param name="ppm" value="5" />
+            <param name="mzabs" value="0.015" />
+            <param name="max_peaks" value="100" />
         </section>
         <section name="diffreport">
-        <conditional name="options">
-            <param name="option" value="show"/>
-            <param name="eicmax" value="200"/>
-            <param name="eicwidth" value="200"/>
-            <param name="value" value="into"/>
-            <param name="h" value="480"/>
-            <param name="w" value="640"/>
-            <param name="mzdec" value="2"/>
-            <param name="sortpval" value="False"/>
-            <param name="tabular2" value="zip"/>
-            <param name="png2" value="zip"/>
-        </conditional>
+            <conditional name="options">
+                <param name="option" value="show" />
+                <param name="eicmax" value="200" />
+                <param name="eicwidth" value="200" />
+                <param name="value" value="into" />
+                <param name="h" value="480" />
+                <param name="w" value="640" />
+                <param name="mzdec" value="2" />
+                <param name="sortpval" value="False" />
+                <param name="tabular2" value="zip" />
+                <param name="png2" value="zip" />
+            </conditional>
         </section>
-        <expand macro="test_peaklist"/>
+        <expand macro="test_peaklist" />
     </xml>
 
     <xml name="test_annotate_quick_false">
-        <param name="quick" value="FALSE"/>
+        <param name="quick" value="FALSE" />
         <section name="groupcorr">
-            <param name="cor_eic_th" value="0.75"/>
-            <param name="graphMethod" value="hcs"/>
-            <param name="pval" value="0.05"/>
-            <param name="calcCiS" value="True"/>
-            <param name="calcIso" value="False"/>
-            <param name="calcCaS" value="False"/>
+            <param name="cor_eic_th" value="0.75" />
+            <param name="graphMethod" value="hcs" />
+            <param name="pval" value="0.05" />
+            <param name="calcCiS" value="True" />
+            <param name="calcIso" value="False" />
+            <param name="calcCaS" value="False" />
         </section>
     </xml>
 
     <xml name="test_annotate_quick_true">
         <conditional name="quick_block">
-            <param name="quick" value="TRUE"/>
+            <param name="quick" value="TRUE" />
         </conditional>
     </xml>
 
@@ -164,24 +161,6 @@
 
     </token>
 
-    <token name="@HELP_CAMERA_NEWVERSION_1480@">
-**Version 2.2.6+camera1.48.0 - 11/06/2021**
-
-- UPGRADE: upgrade the CAMERA version from 1.46.0 to 1.48.0 (see CAMERA News_)
-    </token>
-
-    <token name="@HELP_CAMERA_NEWVERSION_1460@">
-**Version 2.2.6+camera1.46.0 - 12/04/2021**
-
-- UPGRADE: upgrade the CAMERA version from 1.42.0 to 1.46.0 (see CAMERA News_)
-    </token>
-
-    <token name="@HELP_CAMERA_NEWVERSION_1420@">
-**Version 2.2.6+camera1.42.0 - 13/02/2020**
-
-- UPGRADE: upgrade the CAMERA version from 1.38.0 to 1.42.0 (see CAMERA News_)
-    </token>
-
     <xml name="citation">
         <citations>
             <citation type="doi">10.1021/ac202450g</citation>
diff --git a/tools/camera_macro/repository_dependencies.xml b/tools/camera_macro/repository_dependencies.xml
deleted file mode 100644
index d2fa8f255e..0000000000
--- a/tools/camera_macro/repository_dependencies.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0"?>
-<repositories>
-	<repository name="rdata_camera_datatypes" owner="lecorguille" />
-	<repository name="rdata_xcms_datatypes" owner="lecorguille" />
-</repositories>
diff --git a/tools/camera_repository_suite/repository_dependencies.xml b/tools/camera_repository_suite/repository_dependencies.xml
deleted file mode 100644
index ba3a4eb1f0..0000000000
--- a/tools/camera_repository_suite/repository_dependencies.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<repositories>
-	<!--CAMERA tools -->
-	<repository name="camera_annotate" owner="lecorguille"/>
-	<repository  name="camera_combinexsannos" owner="mmonsoor"/>
-</repositories>

From d658b59eb5b5654210790ff43a62ca5690d5980c Mon Sep 17 00:00:00 2001
From: Bjoern Gruening <bjoern.gruening@gmail.com>
Date: Sat, 30 Oct 2021 16:57:03 +0200
Subject: [PATCH 3/4] bump verion

---
 tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml   | 2 +-
 tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml b/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
index c962b5f330..0c7f476c42 100644
--- a/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
+++ b/tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.6+camera@TOOL_VERSION@-galaxy0" profile="21.09">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.2.6+camera@TOOL_VERSION@+galaxy1" profile="21.09">
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
     <macros>
         <import>macros.xml</import>
diff --git a/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml b/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
index 4c8d3087fe..10f010326c 100644
--- a/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
+++ b/tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.6+camera@TOOL_VERSION@-galaxy0" profile="20.09">
+<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.2.6+camera@TOOL_VERSION@+galaxy1" profile="20.09">
     <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations</description>
     <macros>
         <import>macros.xml</import>

From 92611d84168897583c1f1e5618a7f3a36b5d2098 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gildas=20Le=20Corguill=C3=A9?=
 <lecorguille@users.noreply.github.com>
Date: Wed, 3 Nov 2021 09:04:06 +0100
Subject: [PATCH 4/4] Update Galaxy to 21.09 in the CI

---
 .github/workflows/pr.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
index 6e88ee1c82..d3c84b5809 100644
--- a/.github/workflows/pr.yaml
+++ b/.github/workflows/pr.yaml
@@ -2,7 +2,7 @@ name: Galaxy Tool Linting and Tests for push and PR
 on: [push, pull_request]
 env:
   GALAXY_REPO: https://github.com/galaxyproject/galaxy
-  GALAXY_RELEASE: release_20.09
+  GALAXY_RELEASE: release_21.09
   MAX_CHUNKS: 4
 jobs:
   # the setup job does two things: