Mercurial > repos > lecorguille > xcms_fillpeaks
diff abims_xcms_fillPeaks.xml @ 4:2edfa5e1f719 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
| author | lecorguille |
|---|---|
| date | Fri, 08 Apr 2016 10:39:59 -0400 |
| parents | 5a54397dbc97 |
| children | cd351af95d14 |
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--- a/abims_xcms_fillPeaks.xml Mon Feb 22 16:40:19 2016 -0500 +++ b/abims_xcms_fillPeaks.xml Fri Apr 08 10:39:59 2016 -0400 @@ -1,20 +1,16 @@ -<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.5"> +<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.6"> <description>Integrate the signal in the region of that peak group not represented and create a new peak</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> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> <command><![CDATA[ - xcms.r + @COMMAND_XCMS_SCRIPT@ xfunction fillPeaks image $image @@ -22,14 +18,10 @@ method $method - ###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> @@ -40,7 +32,7 @@ <option value="MSW" >MSW</option> </param> <!-- To pass planemo test --> - <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />--> + <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> @@ -52,15 +44,14 @@ <test> <param name="image" value="xset.group.retcor.group.RData"/> <param name="method" value="chrom"/> - <param name="zip_file" value="sacuri.zip"/> - <!--<output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" />--> + <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: 157780 (about 17531 per sample)" /> - <has_text text="Peak Groups: 6761" /> + <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: 199718 (about 49930 per sample)" /> + <has_text text="Peak Groups: 48958" /> <has_text text="Sample classes: bio, blank" /> </assert_contents> </output> @@ -68,20 +59,8 @@ </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.fillPeaks @@ -207,6 +186,11 @@ 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 @@ -225,10 +209,8 @@ ]]></help> - <citations> - <citation type="doi">10.1021/ac051437y</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> + + <expand macro="citation" /> </tool>