Mercurial > repos > lecorguille > xcms_retcor
diff abims_xcms_retcor.xml @ 29:c013ed353a2f draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
| author | lecorguille |
|---|---|
| date | Tue, 13 Feb 2018 04:44:03 -0500 |
| parents | 13885e67b123 |
| children | 4d6f4cd7c3ef |
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--- a/abims_xcms_retcor.xml Thu Oct 26 11:16:24 2017 -0400 +++ b/abims_xcms_retcor.xml Tue Feb 13 04:44:03 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.2.0"> +<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.1.1"> <description>Retention Time Correction using retcor function from xcms R package </description> @@ -15,6 +15,9 @@ xfunction retcor xsetRdataOutput '$xsetRData' + ticspdf '$ticsCorPdf' + bicspdf '$bpcsCorPdf' + rplotspdf '$rplotsPdf' method $methods.method #if $methods.method == "obiwarp": @@ -80,32 +83,19 @@ </conditional> <expand macro="input_file_load"/> - <expand macro="input_tic_bpc_pdf"/> </inputs> <outputs> <data name="xsetRData" format="rdata.xcms.retcor" label="${image.name[:-6]}.retcor.RData" /> - <data name="rplotsPdf" format="pdf" from_work_dir="Rplots.pdf" label="${image.name[:-6]}.retcor.Rplots.pdf"> + <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.retcor.Rplots.pdf"> <filter>(methods['method'] == 'peakgroups')</filter> - <filter>(methods['options']['option'] == 'show')</filter> - <filter>(methods['options']['family'] == 'symmetric')</filter> - <filter>(methods['options']['plottype'] != 'none')</filter> - </data> - <data name="ticsCorPdf" format="pdf" from_work_dir="TICs.pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf"> - <filter>tic_bpc_pdf</filter> + <filter>(options['option'] == 'show')</filter> + <filter>(family == 'symmetric')</filter> + <filter>(plottype != 'none')</filter> </data> - <data name="bpcsCorPdf" format="pdf" from_work_dir="BPCs.pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf"> - <filter>tic_bpc_pdf</filter> - </data> - <collection name="ticsCorrectedTabCollection" type="list" label="TIC corrected tabular"> - <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> - <discover_datasets pattern="(?P<designation>.+)-TIC_corrected_mqc\.out" ext="tabular" /> - </collection> - <collection name="bpcsCorrectedTabCollection" type="list" label="BPC corrected tabular"> - <filter>input.extension not in ["mzxml","mzml","mzdata","netcdf"]</filter> - <discover_datasets pattern="(?P<designation>.+)-BPC_corrected_mqc\.out" ext="tabular" /> - </collection> + <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" /> + <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" /> <data name="log" format="txt" label="xset.log.txt" hidden="true" /> </outputs> @@ -135,15 +125,47 @@ </test>--> <test> <param name="image" value="faahKO.xset.group.RData"/> - <expand macro="test_retcor_param"/> + <param name="methods|method" value="peakgroups"/> + <param name="methods|smooth" value="loess"/> + <param name="methods|extra" value="1"/> + <param name="methods|missing" value="1"/> + <param name="methods|options|option" value="show"/> + <param name="methods|options|span" value="0.2"/> + <param name="methods|options|family" value="gaussian"/> + <param name="methods|options|plottype" value="deviation"/> <expand macro="test_file_load_zip"/> - <expand macro="test_retcor_output" raworcorrected="_corrected" /> + <output name="log"> + <assert_contents> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> + <has_text text="Mass range: 200.1-600 m/z" /> + <has_text text="Peaks: 9251 (about 2313 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: KO, WT" /> + </assert_contents> + </output> </test> <test> <param name="image" value="faahKO-single-class.xset.group.RData"/> - <expand macro="test_retcor_param" /> - <expand macro="test_file_load_single"/> - <expand macro="test_retcor_output" raworcorrected="_corrected" /> + <param name="methods|method" value="peakgroups"/> + <param name="methods|smooth" value="loess"/> + <param name="methods|extra" value="1"/> + <param name="methods|missing" value="1"/> + <param name="methods|options|option" value="show"/> + <param name="methods|options|span" value="0.2"/> + <param name="methods|options|family" value="gaussian"/> + <param name="methods|options|plottype" value="deviation"/> + <expand macro="test_file_load_single"/> + <output name="log"> + <assert_contents> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" /> + <has_text text="Mass range: 200.1-600 m/z" /> + <has_text text="Peaks: 9251 (about 2313 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: KO, WT" /> + </assert_contents> + </output> </test> </tests> @@ -155,6 +177,7 @@ Xcms.retcor =========== +----------- Description ----------- @@ -173,17 +196,18 @@ +----------------- Workflow position ----------------- **Upstream tools** -+------------------------+------------------+--------------------+------------+ -| Name | output file | format | parameter | -+========================+==================+====================+============+ -| xcms.group | xset.group.RData | RData | RData file | -+------------------------+------------------+--------------------+------------+ +========================= ================= ======= ========== +Name output file format parameter +========================= ================= ======= ========== +xcms.group xset.group.RData RData RData file +========================= ================= ======= ========== **Downstream tools** @@ -194,13 +218,14 @@ |xcms.group | xset.retcor.RData| RData | +---------------------------+------------------+--------+ +The output file **xset.retcor.RData** is an RData file. You can continue your analysis using it in **xcms.group** tool as an next step. + + **General schema of the metabolomic workflow** .. image:: xcms_retcor_workflow.png ---------------------------------------------------- - ----------- Input files ----------- @@ -235,11 +260,24 @@ Output files ------------ +xset.group.retcor.TICs_corrected.pdf + + | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step. + +xset.group.retcor.BPCs_corrected.pdf + + | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step + xset.group.retcor.RData: rdata.xcms.retcor format | Rdata file that will be necessary in the **xcms.group** step of the workflow. -@HELP_BCP_TIC@ + +------ + +.. class:: infomark + +The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool. --------------------------------------------------- @@ -256,14 +294,24 @@ Parameters ---------- - | **Method**: peakgroups - | **smooth**: loess - | **extra**: 1 - | **missing**: 5 - | **Advanced options**: show - | **span**: 0.4 - | **family**: gaussian - | **plottype**: deviation + | Method: -> **peakgroups** + | smooth: -> **loess** + | extra: -> **1** + | missing -> **1** + | Advanced options: -> **show** + | span -> **0.2** + | family -> **gaussian** + | plottype -> **deviation** + + +Output files +------------ + + | **1) xset.group.retcor.RData: RData file** + + | **2) Example of an xset.group.retcor.TICs_corrected pdf file** + +.. image:: xcms_retcor.png --------------------------------------------------- @@ -271,9 +319,9 @@ Changelog/News -------------- -**Version 2.2.0 - 19/10/2017** +**Version 2.1.1 - 29/11/2017** -- NEW: The TIC and BPC is new exported as tabular files to be visualized using MultiQC. +- 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 2.1.0 - 03/02/2017**