Mercurial > repos > lecorguille > xcms_retcor
diff abims_xcms_retcor.xml @ 8:4bfef820569b draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author | lecorguille |
---|---|
date | Fri, 07 Apr 2017 07:36:24 -0400 |
parents | bb602a5b8819 |
children | e4e0254a3c0a |
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--- a/abims_xcms_retcor.xml Mon Jan 30 08:53:30 2017 -0500 +++ b/abims_xcms_retcor.xml Fri Apr 07 07:36:24 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.8"> +<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.1.0"> <description>Retention Time Correction using retcor function from xcms R package </description> @@ -11,13 +11,13 @@ <command><![CDATA[ @COMMAND_XCMS_SCRIPT@ - image $image + image '$image' xfunction retcor - xsetRdataOutput $xsetRData - ticspdf $ticsCorPdf - bicspdf $bpcsCorPdf - rplotspdf $rplotsPdf + xsetRdataOutput '$xsetRData' + ticspdf '$ticsCorPdf' + bicspdf '$bpcsCorPdf' + rplotspdf '$rplotsPdf' method $methods.method #if $methods.method == "obiwarp": @@ -33,7 +33,7 @@ #end if #end if - @COMMAND_ZIPFILE_LOAD@ + @COMMAND_FILE_LOAD@ @COMMAND_LOG_EXIT@ ]]></command> @@ -43,7 +43,7 @@ <conditional name="methods"> <param name="method" type="select" label="Method to use for retention time correction" help="[method] See the help section below" > <option value="obiwarp" >obiwarp</option> - <option value="peakgroups" selected="peakgroups">peakgroups</option> + <option value="peakgroups" selected="true">peakgroups</option> </param> <when value="obiwarp"> <param name="profStep" type="float" value="1" label="Step size (in m/z)" help="[profStep] to use for profile generation from the raw data files" /> @@ -82,7 +82,7 @@ </when> </conditional> - <expand macro="zipfile_load"/> + <expand macro="input_file_load"/> </inputs> @@ -133,8 +133,29 @@ <param name="methods|options|span" value="0.2"/> <param name="methods|options|family" value="gaussian"/> <param name="methods|options|plottype" value="deviation"/> - <param name="zipfile_load_conditional|zipfile_load_select" value="yes" /> - <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <expand macro="test_file_load_zip"/> + <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"/> + <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" /> @@ -298,6 +319,10 @@ Changelog/News -------------- +**Version 2.1.0 - 03/02/2017** + +- IMPROVEMENT: xcms.retcor can deal with merged individual data + **Version 2.0.8 - 22/12/2016** - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph