# HG changeset patch
# User bgruening
# Date 1441705125 14400
# Node ID 9e9f85c20d992f1b317e1c0722a2798fed513a5b
# Parent  7faaf4a5e4e1e18d2a65cfaea71452d52a0603c9
Uploaded

diff -r 7faaf4a5e4e1 -r 9e9f85c20d99 diffbind.R
--- a/diffbind.R	Thu Jan 16 04:15:09 2014 -0500
+++ b/diffbind.R	Tue Sep 08 05:38:45 2015 -0400
@@ -27,9 +27,7 @@
     q(status=1);
 }
 
-
 library('DiffBind')
-# used to save to BED, GFF or WIG format
 
 if ( !is.null(opt$plots) ) {
     pdf(opt$plots)
diff -r 7faaf4a5e4e1 -r 9e9f85c20d99 diffbind.xml
--- a/diffbind.xml	Thu Jan 16 04:15:09 2014 -0500
+++ b/diffbind.xml	Tue Sep 08 05:38:45 2015 -0400
@@ -1,41 +1,41 @@
-<tool id="diffbind" name="DiffBind" version="2.0.1">
+<tool id="diffbind" name="DiffBind" version="2.0.2">
     <description> differential binding analysis of ChIP-Seq peak data</description>
     <requirements>
-        <requirement type="binary">Rscript</requirement>
-        <requirement type="R-module">DESeq2</requirement>
-        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
-        <requirement type="package" version="1.0.17">deseq2</requirement>
+        <requirement type="package" version="3.0.3">R</requirement>
+        <requirement type="package" version="1.2.10">deseq2</requirement>
         <requirement type="package" version="1.8.3">diffbind</requirement>
     </requirements>
     <command>
+<![CDATA[
         ## seems that diffbind also needs file extensions to work properly
         #set $counter = 1
         #for $sample in $samples:
-            ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &amp;&amp;
-            ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &amp;&amp;
-            ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &amp;&amp;
-            ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &amp;&amp;
+            ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
+            ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
+            ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
+            ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
             #set $counter = $counter + 1
         #end for
 
-        Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R
+        Rscript $__tool_directory__/diffbind.R
             -i $infile
             -o $outfile
             -p $plots
             -f $format
+]]>
     </command>
     <stdio>
-        <regex match="Execution halted" 
-           source="both" 
-           level="fatal" 
+        <regex match="Execution halted"
+           source="both"
+           level="fatal"
            description="Execution halted." />
-        <regex match="Input-Error 01" 
-           source="both" 
-           level="fatal" 
+        <regex match="Input-Error 01"
+           source="both"
+           level="fatal"
            description="Error in your input parameters: Make sure you only apply factors to selected samples." />
-        <regex match="Error in" 
-           source="both" 
-           level="fatal" 
+        <regex match="Error in"
+           source="both"
+           level="fatal"
            description="An undefined error occured, please check your intput carefully and contact your administrator." />
     </stdio>
     <inputs>
@@ -49,7 +49,7 @@
             <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/>
             <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
         </repeat>
-        <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" 
+        <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
             label="Visualising the analysis results"
             help="output an additional PDF files" />
         <param name="format" type="select" label="Output Format">
@@ -81,21 +81,41 @@
     </outputs>
 
     <help>
-
-.. class:: infomark
-
-**What it does** 
+<![CDATA[
 
 
-------
+**What it does**
+
+Diffbind provides functions for  processing  ChIP-Seq  data  enriched  for  genomic  loci  where  specific  protein/DNA  binding  occurs,  including  peak sets  identified  by  ChIP-Seq  peak  callers  and  aligned  sequence  read  datasets. 
+
+**Input**
+
+- You have to specify your samples. Here is one example:
+
+ID      Tissue  Factor  Condition   Treatment   Replicate   Caller  Intervals
+BT4741  BT474   ER      Resistant   Full-Media  1           raw     1084
+
+- BAM file which contains the mapped sequencing reads can be associated with each
+peakset 
 
-**References** 
+- Control BAM file represents a control dataset
+
+- Peak file: Result of your Peak calling experiment
+
+
+**Output**
 
-DiffBind_ Authors:  Rory Stark, Gordon Brown
+As output format you can choose BED, GFF, WIG.
+
+
+**References**
+
+DiffBind_ Authors:  Rory Stark, Gordon Brown (2011)
 
 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
 
 Wrapper authors: Bjoern Gruening, Pavankumar Videm
 
+]]>
     </help>
 </tool>
diff -r 7faaf4a5e4e1 -r 9e9f85c20d99 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 16 04:15:09 2014 -0500
+++ b/tool_dependencies.xml	Tue Sep 08 05:38:45 2015 -0400
@@ -1,18 +1,17 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="R_3_0_1" version="3.0.1">
-        <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <package name="R" version="3.0.3">
+        <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="deseq2" version="1.0.17">
-        <repository changeset_revision="0e80b1827773" name="package_deseq2_1_0_17" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <package name="deseq2" version="1.2.10">
+        <repository changeset_revision="2d4a7ae561d6" name="package_deseq2_1_2_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-
     <package name="diffbind" version="1.8.3">
         <install version="1.0">
             <actions>
                 <action type="setup_r_environment">
-                    <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
-                        <package name="R_3_0_1" version="3.0.1" />
+                    <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.0.3" />
                     </repository>
                         <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/BiocGenerics_0.8.0.tar.gz</package>
                         <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/IRanges_1.20.6.tar.gz</package>