Mercurial > repos > lecorguille > xcms_retcor
diff abims_xcms_retcor.xml @ 6:fcd93f47dcbf draft
planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
| author | lecorguille |
|---|---|
| date | Thu, 07 Apr 2016 16:04:39 -0400 |
| parents | d0efb2c07577 |
| children | 14242e316953 |
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--- a/abims_xcms_retcor.xml Mon Feb 22 17:05:29 2016 -0500 +++ b/abims_xcms_retcor.xml Thu Apr 07 16:04:39 2016 -0400 @@ -1,20 +1,16 @@ -<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.5"> +<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.6"> <description>Retention Time Correction using retcor function from xcms R package </description> - <requirements> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="binary">Rscript</requirement> - <requirement type="package" version="1.44.0">xcms</requirement> - <requirement type="package" version="2.2.0">xcms_w4m_script</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> + <expand macro="requirements"/> + <expand macro="stdio"/> <command><![CDATA[ - xcms.r + @COMMAND_XCMS_SCRIPT@ image $image xfunction retcor @@ -36,15 +32,10 @@ plottype $methods.options.plottype #end if #end if - ###if $zip_file: - ## zipfile $zip_file - ###end if - ; - return=\$?; - mv log.txt $log; - cat $log; - sh -c "exit \$return" - + #if $zip_file: + zipfile $zip_file + #end if + @COMMAND_LOG_EXIT@ ]]></command> <inputs> @@ -64,6 +55,7 @@ </param> <param name="extra" type="integer" value="1" label="Number of extra peaks to allow in retention time correction correction groups" help="[extra]" /> <param name="missing" type="integer" value="1" label="Number of missing samples to allow in retention time correction groups" help="[missing]" /> + <conditional name="options"> <param name="option" type="select" label="Advanced options"> <option value="show">show</option> @@ -82,14 +74,15 @@ <option value="deviation">deviation</option> <option value="mdevden">mdevden</option> </param> + </when> <when value="hide"> </when> </conditional> </when> </conditional> - <!-- To pass planemo test --> - <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />--> + <!-- To pass planemo test --> + <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." /> </inputs> <outputs> @@ -108,25 +101,21 @@ <tests> <test> <param name="image" value="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"/> - <param name="zip_file" value="sacuri.zip"/> - <!--<output name="xsetRData" file="xset.group.retcor.RData" />--> - <!--<output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />--> - <!--<output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />--> - <!--<output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />--> + <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"/> + <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> <output name="log"> <assert_contents> - <has_text text="object with 9 samples" /> - <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" /> - <has_text text="Mass range: 50.0019-999.9863 m/z" /> - <has_text text="Peaks: 135846 (about 15094 per sample)" /> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" /> + <has_text text="Mass range: 50.0021-999.9863 m/z" /> + <has_text text="Peaks: 59359 (about 14840 per sample)" /> <has_text text="Peak Groups: 0" /> <has_text text="Sample classes: bio, blank" /> </assert_contents> @@ -135,21 +124,8 @@ </tests> <help><![CDATA[ - -.. class:: infomark - -**Authors** Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu - -.. class:: infomark - -**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M] - - | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. - - - ---------------------------------------------------- +@HELP_AUTHORS@ =========== Xcms.retcor @@ -297,6 +273,11 @@ Changelog/News -------------- +**Version 2.0.6 - 04/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + **Version 2.0.5 - 10/02/2016** - BUGFIX: better management of errors. Datasets remained green although the process failed @@ -317,9 +298,7 @@ ]]></help> - <citations> - <citation type="doi">10.1021/ac051437y</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> + + <expand macro="citation" /> </tool>