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cleanup Camera tools #209

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cleanup Camera tools #209

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a778a70
add gitignore additions
bgruening Oct 30, 2021
6dd3e52
changes to camera
bgruening Oct 30, 2021
d658b59
bump verion
bgruening Oct 30, 2021
92611d8
Update Galaxy to 21.09 in the CI
lecorguille Nov 3, 2021
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2 changes: 1 addition & 1 deletion .github/workflows/pr.yaml
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Expand Up @@ -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:
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69 changes: 69 additions & 0 deletions .gitignore
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@@ -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
224 changes: 59 additions & 165 deletions tools/camera_annotate/abims_CAMERA_annotateDiffreport.xml
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1 change: 0 additions & 1 deletion tools/camera_annotate/repository_dependencies.xml
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122 changes: 28 additions & 94 deletions tools/camera_combinexsannos/abims_CAMERA_combinexsAnnos.xml
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@@ -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@+galaxy1" 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" />
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This is needed, because Galaxy does not know that lib.r belongs to the tool. CAMERA_combinexsAnnos.r can be deduced from the command section, but lib.r not. This feature is new and needs the 21.09 Galaxy release.
The advantage is that it will make this tool for in pulsar.

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Good to know!

<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-->
Expand All @@ -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@
Expand Down Expand Up @@ -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
-----------------
Expand Down Expand Up @@ -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>
1 change: 0 additions & 1 deletion tools/camera_combinexsannos/repository_dependencies.xml
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