diff diffbind.xml @ 0:7faaf4a5e4e1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/diffbind.xml	Thu Jan 16 04:15:09 2014 -0500
@@ -0,0 +1,101 @@
+<tool id="diffbind" name="DiffBind" version="2.0.1">
+    <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="1.8.3">diffbind</requirement>
+    </requirements>
+    <command>
+        ## 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;
+            #set $counter = $counter + 1
+        #end for
+
+        Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R
+            -i $infile
+            -o $outfile
+            -p $plots
+            -f $format
+    </command>
+    <stdio>
+        <regex match="Execution halted" 
+           source="both" 
+           level="fatal" 
+           description="Execution halted." />
+        <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" 
+           description="An undefined error occured, please check your intput carefully and contact your administrator." />
+    </stdio>
+    <inputs>
+        <repeat name="samples" title="Samples" min="2">
+            <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
+            <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
+            <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
+            <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
+            <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
+            <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
+            <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" 
+            label="Visualising the analysis results"
+            help="output an additional PDF files" />
+        <param name="format" type="select" label="Output Format">
+            <option value="bed">BED</option>
+            <option value="gff">GFF</option>
+            <option value="wig">WIG</option>
+        </param>
+    </inputs>
+    <configfiles>
+<configfile name="infile">
+SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
+#set $counter = 1
+#for $sample in $samples:
+$sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
+#set $counter = $counter + 1
+#end for
+</configfile>
+    </configfiles>
+    <outputs>
+        <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
+            <change_format>
+                <when input="format" value="wig" format="wig" />
+                <when input="format" value="gff" format="gff" />
+            </change_format>
+        </data>
+        <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
+            <filter>pdf == True</filter>
+        </data>
+    </outputs>
+
+    <help>
+
+.. class:: infomark
+
+**What it does** 
+
+
+------
+
+**References** 
+
+DiffBind_ Authors:  Rory Stark, Gordon Brown
+
+.. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
+
+Wrapper authors: Bjoern Gruening, Pavankumar Videm
+
+    </help>
+</tool>