Mercurial > repos > lecorguille > xcms_xcmsset
diff abims_xcms_xcmsSet.xml @ 6:0888f7ef739a draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
| author | lecorguille |
|---|---|
| date | Fri, 08 Apr 2016 10:38:52 -0400 |
| parents | 588b0a7ae4b0 |
| children | 451ff602a957 |
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--- a/abims_xcms_xcmsSet.xml Mon Feb 22 16:25:05 2016 -0500 +++ b/abims_xcms_xcmsSet.xml Fri Apr 08 10:38:52 2016 -0400 @@ -1,20 +1,16 @@ -<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.7"> +<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.8"> <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </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@ #if $inputs.input == "lib": library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library #elif $inputs.input == "zip_file": @@ -33,16 +29,16 @@ #if $methods.method == "centWave": ppm $methods.ppm peakwidth "c($methods.peakwidth)" - #if $methods.options_scanrange.option == "show": + #if $methods.options_scanrange.option == "show": scanrange "c($methods.options_scanrange.scanrange)" - #end if - #if $methods.options_c.option == "show": - mzdiff $methods.options_c.mzdiff - snthresh $methods.options_c.snthresh - integrate $methods.options_c.integrate - noise $methods.options_c.noise - prefilter "c($methods.options_c.prefilter)" - #end if + #end if + #if $methods.options_c.option == "show": + mzdiff $methods.options_c.mzdiff + snthresh $methods.options_c.snthresh + integrate $methods.options_c.integrate + noise $methods.options_c.noise + prefilter "c($methods.options_c.prefilter)" + #end if #elif $methods.method == "matchedFilter": step $methods.step fwhm $methods.fwhm @@ -62,11 +58,7 @@ scales "c($methods.scales)" SNR.method "$methods.SNR_method" #end if - ; - return=\$?; - mv log.txt $log; - cat $log; - sh -c "exit \$return" + @COMMAND_LOG_EXIT@ ]]></command> <inputs> @@ -192,25 +184,38 @@ <tests> <test> - <param name="inputs.input" value="zip_file" /> - <param name="inputs.zip_file" value="sacuri.zip" /> - <param name="methods.method" value="matchedFilter" /> - <param name="methods.step" value="0.01" /> - <param name="methods.fwhm" value="4" /> - <param name="methods.options_m.option" value="show" /> - <param name="methods.options_m.max" value="50" /> - <param name="methods.options_m.snthresh" value="1" /> - <param name="methods.options_m.steps" value="2" /> - <!--<output name="xsetRData" file="xset.RData" />--> - <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />--> - <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />--> - <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />--> + <param name="inputs|input" value="zip_file" /> + <param name="inputs|zip_file" value="sacuri_dir_root.zip" ftype="zip" /> + <param name="methods|method" value="matchedFilter" /> + <param name="methods|step" value="0.01" /> + <param name="methods|fwhm" value="4" /> + <param name="methods|options_m|option" value="show" /> + <param name="methods|options_m|max" value="50" /> + <param name="methods|options_m|snthresh" value="1" /> + <param name="methods|options_m|steps" value="2" /> <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="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: 0" /> + <has_text text="Sample classes: bio, blank" /> + </assert_contents> + </output> + </test> + <test> + <param name="inputs|input" value="zip_file" /> + <param name="inputs|zip_file" value="sacuri_current_root.zip" ftype="zip" /> + <param name="methods|method" value="centWave" /> + <param name="methods|ppm" value="25" /> + <param name="methods|peakwidth" value="20,50" /> + <output name="log"> + <assert_contents> + <has_text text="object with 4 samples" /> + <has_text text="Time range: 3.5-1139.2 seconds (0.1-19 minutes)" /> + <has_text text="Mass range: 57.9756-593.4086 m/z" /> + <has_text text="Peaks: 1535 (about 384 per sample)" /> <has_text text="Peak Groups: 0" /> <has_text text="Sample classes: bio, blank" /> </assert_contents> @@ -220,17 +225,7 @@ <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.xcmsSet @@ -463,6 +458,10 @@ Changelog/News -------------- +**Version 2.0.8 - 06/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + **Version 2.0.7 - 10/02/2016** @@ -474,7 +473,7 @@ - UPDATE: refactoring of internal management of inputs/outputs -- UPDATE: refactoring to feed the new report tool +- TEST: refactoring to feed the new report tool **Version 2.0.2 - 18/01/2016 @@ -497,10 +496,5 @@ ]]></help> - - <citations> - <citation type="doi">10.1021/ac051437y</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> - + <expand macro="citation" /> </tool>