diff findDMR/findDMR.xml @ 6:a0e3f4efb03f draft

Uploaded

--- a/findDMR/findDMR.xml	Mon Mar 20 06:51:59 2017 -0400
+++ b/findDMR/findDMR.xml	Tue Apr 25 13:19:29 2017 -0400
@@ -1,56 +1,35 @@
-<tool id="DMR" name="findDMR" version="1.16.2">
-  <description>
-from series of samples
-  </description>
+<tool id="findDMR" name="findDMR" version="1.16.2">
   <requirements>
-         <requirement type="package" version="3.2.1">R</requirement>
-     </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 $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</command>
+  <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$output" </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>
+    <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="bed" name="DMR" label="DMR.bed"/>
+    <data format="txt" name="output" label="findDMR.txt"/>
   </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 type="data">
+                <element format="Rdata" name="input1" label="test-data/GenomicRatioSet.Rdata"/>
+                <element format="txt" name="input2" label="test-data/PhenoTab.txt"/>
           </collection>
         </element>
         </param>
-        <output format="bed" name="DMR" label="test-data/DMR.bed"/>
+        <output format="txt" name="output" label="test-data/findDMR.txt"/>
         </test>
     </tests>
   <help>
-**Description**
+Identify CpGs where methylation is associated with a continuous or categorical phenotype.
 </help>
 <citations>
-DMR
+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>