comparison findDMR/findDMR.xml @ 12:083895dbc289 draft

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11:24ac6f93cc3e

<tool id="DMR" name="findDMR" version="1.16.2">
  <description>
from series of samples
  </description>
  <requirements>
    <requirement type= "package" version="0.0.1">450kdependency</requirement>
     <requirement type="package" version="3.2.1">R</requirement>
     </requirements>
<stdio>
   <exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command>
  <inputs>
    <param optional="false" format="txt" name="GSMTable" type="data" value="" help="GSM ID and phenotype table." label="[required] GSMTable">
      <validator type="empty_field" message="This field is required."/>
    </param>
     <param optional="false" format="txt" name="platform" type="data" value="" help="CG, CHR, BP table." label="[required] platform">
      <validator type="empty_field" message="This field is required."/>
    </param>
     <param optional="false" format="txt" name="Data_Table" type="data" value="" help="Matrix of data." label="[required] Data_Table">
      <validator type="empty_field" message="This field is required."/>
    </param>
    <param name="cutoff" type="float" value=""
	       label="Enter cutoff size (number)"
	       help="e.g. '0.2'" >
      </param>
    <param name="clusterSize" type="float" value=""
	       label="Enter cluster size (number)"
	       help="e.g. '2'" >
      </param>
  </inputs>
  <outputs>
    <data format="bed" name="DMR" label="DMR.bed"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data">
          <collection type="data">
              <element name="GSMTable" value="test-data/input.txt"/>
              <element name="platform" value="test-data/platform.txt"/>
              <element name="Data_Table" value="test-data/Data_Table.txt"/>
              <element name="cutoff" value="0.2"/>
              <element name="clusterSize" value="2"/>
          </collection>
        </element>
        </param>
        <output format="bed" name="DMR" label="test-data/DMR.bed"/>
        </test>
    </tests>
  <help>
**Description**
</help>
<citations>
DMR
</citations>
</tool>

12:083895dbc289

<tool id="findDMR" name="findDMR" version="1.16.2">
  <requirements>
   <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
</requirements>
<stdio>
   <exit_code range="1:" />
</stdio>
  <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$output" </command>
  <inputs>
    <param name="input1" format="Rdata" label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/>
    <param name="input2" format="txt" label="PhenoTab.txt" help="ID and Phenotype table"/>
  </inputs>
  <outputs>
    <data format="txt" name="output" label="findDMR.txt"/>
  </outputs>
  <tests>
    <test>
      <param name="test">
      <element name="test-data"/>
           <collection type="data">
                <element format="Rdata" name="input1" label="test-data/GenomicRatioSet.Rdata"/>
                <element format="txt" name="input2" label="test-data/PhenoTab.txt"/>
          </collection>
        </param>
        <output format="txt" name="output" label="test-data/findDMR.txt"/>
        </test>
    </tests>
  <help>
Identify CpGs where methylation is associated with a continuous or categorical phenotype.
</help>
<citations>
Aryee, Martin J., et al. "Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays." Bioinformatics 30.10 (2014): 1363-1369.
</citations>
</tool>