annotate findDMR/findDMR.xml @ 3:42cfcac7779d draft

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author testtool
date Mon, 06 Feb 2017 10:44:03 -0500
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1 <tool id="DMR" name="findDMR" version="1.16.2">
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2 <description>
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3 from series of samples
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="3.2.1">R</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$IlmnTable" "$gmTable" "$cutoff" "$clusterSize" "$DMR"</command>
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12 <inputs>
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13 <param optional="false" format="csv" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable">
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14 <validator type="empty_field" message="This field is required."/>
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15 </param>
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16 <param optional="false" format="csv" name="IlmnTable" type="data" value="" help="CG, CHR, BP table." label="[required] IlmnTable">
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17 <validator type="empty_field" message="This field is required."/>
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18 </param>
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19 <param optional="false" format="csv" name="gmTable" type="data" value="" help="gmSet of data." label="[required] gmTable">
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20 <validator type="empty_field" message="This field is required."/>
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21 </param>
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22 <param name="cutoff" type="float" value=""
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23 label="Enter cutoff size (number)"
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24 help="e.g. '0.2'" >
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25 </param>
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26 <param name="clusterSize" type="float" value=""
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27 label="Enter cluster size (number)"
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28 help="e.g. '2'" >
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29 </param>
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30 </inputs>
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31 <outputs>
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32 <data format="bed" name="DMR" label="DMR.bed"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="test">
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37 <element name="test-data">
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38 <collection type="data">
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39 <element name="GSMTable" value="test-data/input.csv"/>
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40 <element name="IlmnTable" value="test-data/IlmnTable.csv"/>
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41 <element name="gmTable" value="test-data/gmTable.csv"/>
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42 <element name="cutoff" value="0.2"/>
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43 <element name="clusterSize" value="2"/>
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44 </collection>
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45 </element>
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46 </param>
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47 <output format="bed" name="DMR" label="test-data/DMR.bed"/>
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48 </test>
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49 </tests>
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50 <help>
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51 **Description**
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52 </help>
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53 <citations>
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54 DMR
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55 </citations>
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56 </tool>