Mercurial > repos > lecorguille > xcms_group
diff abims_xcms_group.xml @ 4:2db1d1d0f131 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
author | lecorguille |
---|---|
date | Fri, 08 Apr 2016 10:39:09 -0400 |
parents | 98e33cdf0eb1 |
children | 0306a96cc446 |
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--- a/abims_xcms_group.xml Mon Feb 22 16:31:48 2016 -0500 +++ b/abims_xcms_group.xml Fri Apr 08 10:39:09 2016 -0400 @@ -1,20 +1,16 @@ -<tool id="abims_xcms_group" name="xcms.group" version="2.0.4"> +<tool id="abims_xcms_group" name="xcms.group" version="2.0.5"> <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</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@ xfunction group image $image @@ -41,12 +37,7 @@ rtCheck $methods.rtCheck kNN $methods.kNN #end if - ; - return=\$?; - mv log.txt $log; - cat $log; - sh -c "exit \$return" - + @COMMAND_LOG_EXIT@ ]]></command> <inputs> @@ -109,41 +100,47 @@ <tests> <test> <param name="image" value="xset.RData"/> - <param name="methods.method" value="density"/> - <param name="methods.bw" value="5"/> - <param name="methods.minfrac" value="0.3"/> - <param name="methods.mzwid" value="0.01"/> - <param name="methods.density_options.option" value="show"/> - <param name="methods.density_options.max" value="50"/> - <!--<output name="xsetRData" file="xset.group.RData" />--> - <!--<output name="rplotsPdf" file="xset.group.Rplots.pdf" />--> + <param name="methods|method" value="density"/> + <param name="methods|bw" value="5"/> + <param name="methods|minfrac" value="0.3"/> + <param name="methods|mzwid" value="0.01"/> + <param name="methods|density_options|option" value="show"/> + <param name="methods|density_options|max" value="50"/> <output name="log"> <assert_contents> - <has_text text="object with 9 samples" /> - <has_text text="Time range: 0.7-1140 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="Peak Groups: 6642" /> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 0.7-1139.7 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: 48998" /> <has_text text="Sample classes: bio, blank" /> </assert_contents> </output> - + </test> + <test> + <param name="image" value="xset.group.retcor.RData"/> + <param name="methods|method" value="density"/> + <param name="methods|bw" value="5"/> + <param name="methods|minfrac" value="0.3"/> + <param name="methods|mzwid" value="0.01"/> + <param name="methods|density_options|option" value="show"/> + <param name="methods|density_options|max" value="50"/> + <output name="log"> + <assert_contents> + <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: 48958" /> + <has_text text="Sample classes: bio, blank" /> + </assert_contents> + </output> </test> </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 - -**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.Group @@ -277,6 +274,11 @@ Changelog/News -------------- +**Version 2.0.5 - 04/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + **Version 2.0.4 - 10/02/2016** - BUGFIX: better management of errors. Datasets remained green although the process failed @@ -296,10 +298,7 @@ ]]></help> - <citations> - <citation type="doi">10.1021/ac051437y</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> + <expand macro="citation" /> </tool>