annotate annotate_peak/annotatePeak.xml @ 20:2044ad2c1c93 draft default tip

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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>