# HG changeset patch
# User bgruening
# Date 1456511728 18000
# Node ID aefe2a771a95a52e05f8f47f110b2497a3d9f06d
# Parent  4de6355eca006ea743167c623a1f6845c57cfa1f
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty

diff -r 4de6355eca00 -r aefe2a771a95 diffbind.tar.bz2
Binary file diffbind.tar.bz2 has changed
diff -r 4de6355eca00 -r aefe2a771a95 diffbind.xml
--- a/diffbind.xml	Sat Mar 15 05:21:59 2014 -0400
+++ b/diffbind.xml	Fri Feb 26 13:35:28 2016 -0500
@@ -6,37 +6,38 @@
         <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>
-        <requirement type="set_environment">DIFFBIND_SCRIPT_PATH</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 \$DIFFBIND_SCRIPT_PATH/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>
@@ -50,7 +51,7 @@
             <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">
@@ -82,21 +83,41 @@
     </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 4de6355eca00 -r aefe2a771a95 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Mar 15 05:21:59 2014 -0400
+++ b/tool_dependencies.xml	Fri Feb 26 13:35:28 2016 -0500
@@ -1,19 +1,16 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="3.0.3">
-        <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="9a289bea9051" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deseq2" version="1.2.10">
-        <repository changeset_revision="2d3eb2823bf7" name="package_deseq2_1_2_10" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="e8df6ebba5ff" name="package_deseq2_1_2_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <set_environment version="1.0">
-        <environment_variable action="set_to" name="DIFFBIND_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
     <package name="diffbind" version="1.8.3">
         <install version="1.0">
             <actions>
                 <action type="setup_r_environment">
-                    <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="9a289bea9051" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.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>