# HG changeset patch
# User testtool
# Date 1497280173 14400
# Node ID 9de797a673ad9d73041fdbfe843551350034087d
# Parent  3735f4bd0a2d0923695f03902cf5b0cccda43759
Uploaded

diff -r 3735f4bd0a2d -r 9de797a673ad findDMR/findDMR.xml
--- a/findDMR/findDMR.xml	Mon Jun 12 11:05:56 2017 -0400
+++ b/findDMR/findDMR.xml	Mon Jun 12 11:09:33 2017 -0400
@@ -1,34 +1,53 @@
-<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>
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="findDMR" name="findDMR" version="1.20.0">
+<requirements>
+<requirement type="package" version="1.20.0">bioconductor-minfi</requirement>
 </requirements>
 <stdio>
-   <exit_code range="1:" />
+<exit_code range="1:" />
 </stdio>
-  <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$output" </command>
+  <command> Rscript $__tool_directory__/findDMR.R "$input1" "$input2" "$cutoff" "$B"  "$pickCutoffQ" "$output1"  "$output2"</command>
   <inputs>
-    <param name="input1" type="data" format="Rdata" label="GenomicRatioSet.Rdata" help="e.g. 'GSE51547'"/>
-    <param name="input2" type="data" format="txt" label="PhenoTab.txt" help="ID and Phenotype table"/>
+    <param format="RDdata" name="input1" type="data" label="Genomic Ratio Set" help="e.g. 'GRsetFromGEO tool output'"/>
+    <param format="csv" name="input2" type="data" label="Phenotype Table"
+      help="e.g.'ID Phenotype
+      GSM1255789       OLD
+      GSM1255798       OLD
+      GSM1255778      YOUNG'"/>
+    <param name="cutoff" type="text" value="0.5" label="Cutoff" help="A  v. Values of the estimate of the genomic profile above the cutoff or below the negative of the cutoff will be used as candidate regions. It is possible to give two separate values (upper and lower bounds). If one value is given, the lower bound is minus the value."/>
+     <param name="B" type="text" value="0" label="Number of resamples" help="An integer denoting the number of resamples to use when computing null distributions. This defaults to 0. If permutations is supplied that defines the number of permutations/bootstraps and B is ignored."/>
+     <param name="pickCutoffQ" type="text" value="0.99" label="pickCutoffQ" help="The quantile used for picking the cutoff using the permutation distribution."/>
   </inputs>
   <outputs>
-    <data format="txt" name="output" label="findDMR.txt"/>
+    <data format="text" type="data" name="output1" label="DMR.txt"/>
+    <data format="bed" type="data" name="output2" 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="input1" type="data" format="RData" label="test-data/out.RData"/>
+            <element name="input2" type="data" format="csv" label="test-data/OLDvsYOUNG.csv"/>
+                <element name="cutoff" value="0.5"/>
+                <element name="B" value="0"/>
+                <element name="pickCutoffQ" value="0.99"/>
           </collection>
+        </element>
         </param>
-        <output format="txt" name="output" label="test-data/findDMR.txt"/>
+        <output name="output1" type="data" format="text" label="test-data/DMR.txt"/>
+        <output name="output2" type="data" format="bed" label="test-data/DMR.bed"/>
         </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>
+**What it does**
+This R-based tool look for genomic regions that are differentially methylated between two conditions
+**Input**
+GenomicRatioSet object
+**Output**
+Text and BED file containing differentially methylated regions
+  </help>
+  <citations>
+<citation type="doi">10.1093/bioinformatics/btu049</citation>
+  </citations>
 </tool>