Mercurial > repos > lecorguille > xcms_summary
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author | lecorguille |
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date | Wed, 24 Feb 2016 12:32:32 -0500 |
parents | 930478b22633 |
children | df7b3b846cb6 |
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<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.0"> <description>Create a summary of XCMS 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="1.22.0">camera</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" /> </stdio> <command interpreter="Rscript"><![CDATA[ xcms_summary.r image $image htmlOutput $htmlOutput user_email $__user_email__ ]]></command> <inputs> <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" /> </inputs> <outputs> <data name="htmlOutput" format="html" label="xcms summary html" /> </outputs> <tests> <test> <param name="image" value="fillpeaks.RData" /> <output name="htmlOutput" file="summary.html" /> </test> </tests> <help><![CDATA[ .. class:: infomark **Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff part of Workflow4Metabolomics.org [W4M] | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. --------------------------------------------------- ============ Xcms.summary ============ ----------- Description ----------- This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools --------------------------------------------------- Changelog/News -------------- **Version 1.0.0 - 10/02/2016** - NEW: Create a summary of XCMS analysis ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btu813</citation> </citations> </tool>