Mercurial > repos > lecorguille > xcms_summary
view abims_xcms_summary.xml @ 12:27e7da5f6848 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
author | lecorguille |
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date | Fri, 07 Apr 2017 07:37:23 -0400 |
parents | cb599006715f |
children | 4c757d1ba7b4 |
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<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.3"> <description>Create a summary of XCMS analysis</description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="1.26.0">bioconductor-camera</requirement> <requirement type="package" version="1.1_4">r-batch</requirement> </requirements> <expand macro="stdio"/> <command><![CDATA[ $__tool_directory__/xcms_summary.r image '$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="faahKO.xset.group.retcor.group.fillpeaks.RData" /> <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" /> </test> <test> <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" /> <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" /> </test> </tests> <help><![CDATA[ @HELP_AUTHORS@ ============ Xcms.summary ============ ----------- Description ----------- This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools ----------------- Workflow position ----------------- **Upstream tools** ========================= ================= ===================== ========== Name output file format parameter ========================= ================= ===================== ========== xcms.xcmsSet xset.RData rdata.xcms.raw RData file ------------------------- ----------------- --------------------- ---------- xcms.group xset.RData rdata.xcms.group RData file ------------------------- ----------------- --------------------- ---------- xcms.retcor xset.RData rdata.xcms.retcor RData file ------------------------- ----------------- --------------------- ---------- xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file ------------------------- ----------------- --------------------- ---------- CAMERA.annotate xset.RData rdata.camera.* RData file ========================= ================= ===================== ========== .. image:: xcms_summary_workflow.png --------------------------------------------------- Changelog/News -------------- **Version 1.0.3 - 03/02/2017** - IMPROVEMENT: xcms.summary can deal with merged individual data **Version 1.0.2 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 **Version 1.0.1 - 04/04/2016** - TEST: refactoring to pass planemo test using conda dependencies **Version 1.0.0 - 10/02/2016** - NEW: Create a summary of XCMS analysis ]]></help> <expand macro="citation" /> </tool>