workflow4metabolomics · lecorguille · Sep 11, 2023 · May 12, 2023 · May 12, 2023 · May 12, 2023
diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -43,7 +43,7 @@ jobs:
         echo 'event.after: ${{ github.event.after }}'
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
-      run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"
+      run: echo "galaxy-head-sha=$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)" >> $GITHUB_OUTPUT
     - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
@@ -115,6 +115,7 @@ jobs:
       id: lint
       with:
         mode: lint
+        fail-level: warn
         repository-list: ${{ needs.setup.outputs.repository-list }}
         tool-list: ${{ needs.setup.outputs.tool-list }}
     - uses: actions/upload-artifact@v3
@@ -311,7 +312,7 @@ jobs:
   combine_outputs:
     name: Combine chunked test results
     needs: [setup, test]
-    if: ${{ needs.setup.outputs.repository-list != '' }}
+    if: ${{ always() && needs.setup.outputs.repository-list != '' }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -344,6 +345,12 @@ jobs:
       id: check
       with:
         mode: check
+    - name: Check if all test chunks succeeded
+      run: |
+        NFILES=$(ls artifacts/ | grep "Tool test output" | wc -l)
+        if [[ "${{ needs.setup.outputs.chunk-count }}" != "$NFILES" ]]; then
+          exit 1
+        fi
 
   # deploy the tools to the toolsheds (first TTS for testing)
   deploy:

diff --git a/datatypes/datatype_no_unzip/.shed.yml → ...ted/datatypes/datatype_no_unzip/.shed.yml b/datatypes/datatype_no_unzip/.shed.yml → ...ted/datatypes/datatype_no_unzip/.shed.yml
diff --git a/datatypes/datatype_no_unzip/README → ...ecated/datatypes/datatype_no_unzip/README b/datatypes/datatype_no_unzip/README → ...ecated/datatypes/datatype_no_unzip/README
diff --git a/...ypes/datatype_no_unzip/datatypes_conf.xml → ...ypes/datatype_no_unzip/datatypes_conf.xml b/...ypes/datatype_no_unzip/datatypes_conf.xml → ...ypes/datatype_no_unzip/datatypes_conf.xml
diff --git a/...s/datatype_no_unzip/no_unzip_datatypes.py → ...s/datatype_no_unzip/no_unzip_datatypes.py b/...s/datatype_no_unzip/no_unzip_datatypes.py → ...s/datatype_no_unzip/no_unzip_datatypes.py
diff --git a/datatypes/datatype_rdata_camera/.shed.yml → ...datatypes/datatype_rdata_camera/.shed.yml b/datatypes/datatype_rdata_camera/.shed.yml → ...datatypes/datatype_rdata_camera/.shed.yml
diff --git a/.../datatype_rdata_camera/datatypes_conf.xml → .../datatype_rdata_camera/datatypes_conf.xml b/.../datatype_rdata_camera/datatypes_conf.xml → .../datatype_rdata_camera/datatypes_conf.xml
diff --git a/...ype_rdata_camera/rdata_camera_datatype.py → ...ype_rdata_camera/rdata_camera_datatype.py b/...ype_rdata_camera/rdata_camera_datatype.py → ...ype_rdata_camera/rdata_camera_datatype.py
diff --git a/datatypes/datatype_rdata_xcms/.shed.yml → ...d/datatypes/datatype_rdata_xcms/.shed.yml b/datatypes/datatype_rdata_xcms/.shed.yml → ...d/datatypes/datatype_rdata_xcms/.shed.yml
diff --git a/...es/datatype_rdata_xcms/datatypes_conf.xml → ...es/datatype_rdata_xcms/datatypes_conf.xml b/...es/datatype_rdata_xcms/datatypes_conf.xml → ...es/datatype_rdata_xcms/datatypes_conf.xml
diff --git a/...atatype_rdata_xcms/rdata_xcms_datatype.py → ...atatype_rdata_xcms/rdata_xcms_datatype.py b/...atatype_rdata_xcms/rdata_xcms_datatype.py → ...atatype_rdata_xcms/rdata_xcms_datatype.py
diff --git a/datatypes/datatype_zip/.shed.yml → deprecated/datatypes/datatype_zip/.shed.yml b/datatypes/datatype_zip/.shed.yml → deprecated/datatypes/datatype_zip/.shed.yml
diff --git a/datatypes/datatype_zip/datatypes_conf.xml → ...datatypes/datatype_zip/datatypes_conf.xml b/datatypes/datatype_zip/datatypes_conf.xml → ...datatypes/datatype_zip/datatypes_conf.xml
diff --git a/tools/msnbase_readmsdata/.shed.yml b/tools/msnbase_readmsdata/.shed.yml
diff --git a/tools/msnbase_readmsdata/README.rst b/tools/msnbase_readmsdata/README.rst
diff --git a/tools/msnbase_readmsdata/lib.r b/tools/msnbase_readmsdata/lib.r
diff --git a/tools/msnbase_readmsdata/macros.xml b/tools/msnbase_readmsdata/macros.xml
diff --git a/tools/msnbase_readmsdata/macros_msnbase.xml b/tools/msnbase_readmsdata/macros_msnbase.xml
diff --git a/tools/msnbase_readmsdata/repository_dependencies.xml b/tools/msnbase_readmsdata/repository_dependencies.xml
diff --git a/tools/msnbase_readmsdata/test-data/faahKO_reduce.zip b/tools/msnbase_readmsdata/test-data/faahKO_reduce.zip
diff --git a/tools/msnbase_readmsdata/test-data/ko15.CDF b/tools/msnbase_readmsdata/test-data/ko15.CDF
@@ -0,0 +1,124 @@
+definitions:
+  include: &default-includes
+    - test-data
+    - static
+    - lib.r
+    - macros_xcms.xml
+    - macros.xml
+
+name: xcms
+owner: workflow4metabolomics
+remote_repository_url: https://github.com/workflow4metabolomics/tools-metabolomics/
+homepage_url: https://github.com/sneumann/xcms
+categories:
+- Metabolomics
+
+repositories:
+  xcms_export_samplemetadata:
+    description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Get a sample metadata file'
+    long_description: |
+      Generates a skeleton of sampleMetadata
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: lecorguille
+    include:
+      [*default-includes, xcms_export_samplemetadata.xml, xcms_export_samplemetadata.r]
+  xcms_fillpeaks:
+    description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Integrate areas of missing peaks'
+    long_description: |
+      For each sample, identify peak groups where that sample is not represented.
+      For each of those peak groups, integrate the signal in the region of that peak group and create a new peak.
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: lecorguille
+    include:
+      [*default-includes, abims_xcms_fillPeaks.xml, xcms_fillpeaks.r]
+  xcms_group:
+    description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Group peaks from different samples together'
+    long_description: |
+      Group peaks together across samples using overlapping m/z bins and
+      calculation of smoothed peak distributions in chromatographic time.
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: lecorguille
+    include:
+      [*default-includes, abims_xcms_group.xml, xcms_group.r]
+  xcms_merge:
+    description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Merge individual xcmsSet outputs'
+    long_description: |
+      Filtration and Peak Identification using xcmsSet function from xcms R
+      package to preprocess LC/MS data for relative quantification and
+      statistical analysis
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: lecorguille
+    include:
+      [*default-includes, xcms_merge.xml, xcms_merge.r]
+  xcms_plot_chromatogram:
+    description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC)'
+    long_description: |
+      Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC)
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: lecorguille
+    include:
+      [*default-includes, xcms_plot_chromatogram.xml, xcms_plot_chromatogram.r]
+  xcms_refine:
+    description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Refine choice of peaks'
+    long_description: |
+      Remove or merge chromatographic peaks based on specific criteria.
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: workflow4metabolomics
+    include:
+      [*default-includes, abims_xcms_refine.xml, xcms_refine.r]
+  xcms_retcor:
+    description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples'
+    long_description: |
+      Retention Time Correction using retcor function from xcms R package
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: lecorguille
+    include:
+      [*default-includes, abims_xcms_refine.xml, xcms_refine.r]
+  xcms_xcmsset:
+    description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - peaks calling in NetCDF/mzXML files'
+    long_description: |
+      Filtration and Peak Identification using xcmsSet function from xcms R
+      package to preprocess LC/MS data for relative quantification and
+      statistical analysis
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: lecorguille
+    include:
+      [*default-includes, abims_xcms_xcmsSet.xml, xcms_xcmsSet.r]
+  xcms_summary:
+    description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS and CAMERA analysis'
+    long_description: |
+      This tool create a HTML summary of XCMS and CAMERA analysis
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: lecorguille
+    include:
+      [*default-includes, abims_xcms_summary.xml, xcms_summary.r]
+  msnbase_readmsdata:
+    description: '[Metabolomics][W4M][LC-MS] MSnbase R Package - Preprocessing - Imports Mass-Spectrometry Data Files'
+    long_description: |
+      Reads XML-based mass-spectrometry data files.  Can be chained with the W4M
+      xcms.findChromPeaks tool
+      Part of the W4M project: http://workflow4metabolomics.org
+      XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html 
+    owner: lecorguille
+    include:
+      [*default-includes, msnbase_readmsdata.xml, msnbase_readmsdata.r, macros_msnbase.xml]
+
+suite:
+  name: suite_xcms
+  owner: lecorguille
+  homepage_url: http://workflow4metabolomics.org
+  description: '[Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Framework for processing data for high-throughput, untargeted analyte profiling'
+  long_description: |
+    Part of the W4M project: http://workflow4metabolomics.org XCMS:
+    http://www.bioconductor.org/packages/release/bioc/html/xcms.html
+    XCMS: processing mass spectrometry data for metabolite profiling
+    using nonlinear peak alignment, matching, and identification
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@TOOL_VERSION@+galaxy0">
+<tool id="abims_xcms_fillPeaks" name="xcms fillChromPeaks (fillPeaks)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
 
     <description>Integrate areas of missing peaks</description>
 
@@ -128,7 +128,7 @@
             <output name="variableMetadata" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.variableMetadata.tsv" />
             <output name="dataMatrix" file="faahKO.xset.group2.retcor2.group2.fillPeaks2.dataMatrix.tsv" />
         </test>-->
-        <test>
+        <test expect_num_outputs="3">
             <param name="image" value="faahKO-single-class.xset.merged.group.retcor.group.RData" ftype="rdata"/>
             <section name="peaklist">
                 <param name="peaklistBool" value="true" />

@@ -1,4 +1,4 @@
-<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy0">
+<tool id="abims_xcms_group" name="xcms groupChromPeaks (group)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
 
     <description>Perform the correspondence, the grouping of chromatographic peaks within and between samples.</description>
 
@@ -203,7 +203,7 @@
         </test>
         -->
         <!-- from retcor -->
-        <test>
+        <test expect_num_outputs="4">
             <param name="image" value="faahKO-single-class.xset.merged.group.retcor.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="PeakDensity"/>

@@ -1,4 +1,4 @@
-<tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="3.12.0+galaxy0">
+<tool id="abims_xcms_refine" name="xcms refineChromPeaks (refine)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
 
     <description>Remove or merge chromatographic peaks based on specific criteria.</description>
 
@@ -77,7 +77,7 @@
             test 1 - MergeNeighboringPeaks method
         -->
         <test>
-            <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
+            <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="MergeNeighboringPeaks"/>
                 <param name="expandRt" value="2" />
@@ -104,7 +104,7 @@
             test 2 - FilterIntensity method
         -->
         <test>
-            <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
+            <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="FilterIntensity"/>
                 <param name="threshold" value="1e5" />
@@ -126,7 +126,7 @@
             test 3 - CleanPeaks method
         -->
         <test>
-            <param name="image" value="faahKO-single.xset.merged.RData" ftype="rdata"/>
+            <param name="image" value="faahKO-single-class.xset.merged.group.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="CleanPeaks"/>
                 <param name="maxPeakwidth" value="8" />
@@ -244,7 +244,7 @@ xset.RData: rdata.xcms.findchrompeaks format
 Changelog/News
 --------------
 
-.. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
+.. _news: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
 
 
 **Version 3.6.1.0 - 08/02/2021**

@@ -1,4 +1,4 @@
-<tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@TOOL_VERSION@+galaxy0">
+<tool id="abims_xcms_retcor" name="xcms adjustRtime (retcor)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
 
     <description>Retention Time Correction</description>
 

@@ -1,4 +1,4 @@
-<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy0">
+<tool id="abims_xcms_summary" name="xcms process history" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
 
     <description>Create a summary of XCMS analysis</description>
 
@@ -41,7 +41,7 @@
         </test>-->
         <test>
             <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
-            <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" />
+            <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" lines_diff="2"/>
         </test>
     </tests>
 
@@ -82,6 +82,8 @@ CAMERA.annotate           ``*``.annotate.*.RData      rdata.camera.``*``
 
 .. image:: xcms_summary_workflow.png
 
+@HELP_XCMS_MANUAL@
+
 ---------------------------------------------------
 
 Changelog/News

@@ -1,4 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy0">
+<tool id="abims_xcms_xcmsSet" name="xcms findChromPeaks (xcmsSet)" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Chromatographic peak detection</description>
 
     <macros>
@@ -187,11 +187,8 @@
     <outputs>
         <data name="xsetRData" format="rdata.xcms.findchrompeaks" label="${image.name.rsplit('.',1)[0]}.xset.RData" from_work_dir="xcmsSet.RData" />
         <data name="log" format="txt" label="${image.name.rsplit('.',1)[0]}.xset.log.txt" from_work_dir="log.txt" />
-        <data name="peaklist_out1" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" >
-            <filter>methods['method'] == 'CentWave' and (methods['CentWaveAdv']['peaklist'])</filter>
-        </data>
-        <data name="peaklist_out2" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" >
-            <filter>methods['method'] == 'MatchedFilter' and (methods['MatchedFilterAdv']['peaklist'])</filter>
+        <data name="peaklist_out" format="tabular" label="${image.name[:-6]}.chromPeak_table.tsv" from_work_dir="chromPeak_table.tsv" >
+            <filter>methods['method'] in ['CentWave', 'MatchedFilter'] and (methods['CentWaveAdv']['peaklist'])</filter>
         </data>
     </outputs>
 
@@ -227,7 +224,7 @@
                 <has_text text="Sample classes: KO, WT" />
             </assert_stdout>
         </test>-->
-        <test>
+        <test expect_num_outputs="2">
             <param name="image" value="ko15-raw.RData" ftype="rdata" />
             <conditional name="methods">
                 <param name="method" value="CentWave" />