diff findDMR/findDMR.xml @ 10:7df2b7d79391 draft

Uploaded

--- a/findDMR/findDMR.xml	Tue Apr 25 13:35:53 2017 -0400
+++ b/findDMR/findDMR.xml	Thu May 11 11:15:33 2017 -0400
@@ -1,34 +1,57 @@
-<tool id="findDMR" name="findDMR" version="1.16.2">
+<tool id="DMR" name="findDMR" version="1.16.2">
+  <description>
+from series of samples
+  </description>
   <requirements>
-   <requirement name="package_r_3_2_1" type="package" version="3.2.1">R</requirement>
-</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 $__tool_directory__/findDMR.R "$input1" "$input2" "$output" </command>
+  <command> Rscript $__tool_directory__/findDMR.R "$GSMTable" "$platform" "$Data_Table" "$cutoff" "$clusterSize" "$DMR"</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"/>
+    <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="txt" name="output" label="findDMR.txt"/>
+    <data format="bed" name="DMR" label="DMR.bed"/>
   </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"/>
+      <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="txt" name="output" label="test-data/findDMR.txt"/>
+        <output format="bed" name="DMR" label="test-data/DMR.bed"/>
         </test>
     </tests>
   <help>
-Identify CpGs where methylation is associated with a continuous or categorical phenotype.
+**Description**
 </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.
+DMR
 </citations>
 </tool>