Mercurial > repos > testtool > annotate_peak
view annotate_peak/annotatePeak.xml @ 20:2044ad2c1c93 draft default tip
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author | testtool |
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date | Mon, 20 Mar 2017 07:39:23 -0400 |
parents | 741b192da59c |
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<tool id="AP" name="annotatePeak" version="1.16.2"> <requirements> <requirement type="package" version="3.2.1">R</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command> Rscript $__tool_directory__/annotatePeak.R "$DMR" "$annoData" "$bindingType" "$upstream" "$downstream" "$ignore" "$annoPeakTable"</command> <inputs> <param optional="false" format="bed" name="DMR" type="data" value="" help="Bumphunter peaks." label="[required] file"> <validator type="empty_field" message="This field is required."/> </param> <param name="annoData" type="select" label="annoData" help="choose your annoData human or mice"> <option name="human" type="text" value="EnsDb.Hsapiens.v75">Human</option> <option name="mice" type="text" value="EnsDb.Mmusculus.v75">Mice</option> </param> <param name="bindingType" type="select" label="bindingType" help="choose bindingType"> <option name="sS" type="text" value="startSite">startSite</option> <option name="eS" type="text" value="endSite">endSite</option> <option name="fR" type="text" value="fullRange">fullRange</option> </param> <param name="ignore" type="select" label="ignore.peak.strand" help="choose TRUE or FALSE"> <option name="T" type="text" value="TRUE">true</option> <option name="F" type="text" value="FALSE">false</option> </param> <param name="upstream" type="text" value="" label="upstream - number no bigger than 0" help="e.g. '-5000'" > </param> <param name="downstream" type="text" value="" label="downstream - number no less than 1" help="e.g. '5000'" > </param> </inputs> <outputs> <data format="txt" name="annoPeakTable" label="peakAnno.txt"/> </outputs> <tests> <test> <param name="test"> <element name="test-data"> <collection type="data"> <element name="DMR" value="test-data/DMR.bed"/> </collection> </element> </param> <output format="txt" name="annoPeakTable" label="test-data/annoPeakTable.txt"/> </test> </tests> <help> **Description** </help> <citations> DMR </citations> </tool>