# HG changeset patch
# User bgruening
# Date 1389740840 18000
# Node ID 20c431b4cf746deda190cc84cf27739779bfdaaa
# Parent  7929c8b3f6f92b4f6528eaa8e199368e5a8d74e0
Uploaded

diff -r 7929c8b3f6f9 -r 20c431b4cf74 diffbind.R
--- a/diffbind.R	Tue Jan 14 08:13:24 2014 -0500
+++ b/diffbind.R	Tue Jan 14 18:07:20 2014 -0500
@@ -23,8 +23,8 @@
 # if help was asked for print a friendly message
 # and exit with a non-zero error code
 if ( !is.null(opt$help) ) {
-	cat(getopt(spec, usage=TRUE));
-	q(status=1);
+    cat(getopt(spec, usage=TRUE));
+    q(status=1);
 }
 
 
@@ -33,11 +33,11 @@
 library('rtracklayer')
 
 if ( !is.null(opt$plots) ) {
-	pdf(opt$plots)
+    pdf(opt$plots)
 }
 
 
-sample = dba(sampleSheet=opt$infile)
+sample = dba(sampleSheet=opt$infile, peakFormat='bed')
 sample_count = dba.count(sample)
 sample_contrast = dba.contrast(sample_count, categories=DBA_CONDITION)
 sample_analyze = dba.analyze(sample_contrast)
diff -r 7929c8b3f6f9 -r 20c431b4cf74 diffbind.xml
--- a/diffbind.xml	Tue Jan 14 08:13:24 2014 -0500
+++ b/diffbind.xml	Tue Jan 14 18:07:20 2014 -0500
@@ -13,6 +13,8 @@
             -o $outfile
             -p $plots
             -f $format
+        ;
+        cat $infile;
     </command>
     <stdio>
         <regex match="Execution halted" 
@@ -49,12 +51,12 @@
         </param>
     </inputs>
     <configfiles>
-        <configfile name="infile">
+<configfile name="infile">
 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
 #for $sample in $samples:
 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,$sample.bamreads,$sample.bamcontrol,$sample.peaks
 #end for
-        </configfile>
+</configfile>
     </configfiles>
     <outputs>
         <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
@@ -63,7 +65,7 @@
                 <when input="format" value="gff" format="gff" />
             </change_format>
         </data>
-        <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
+        <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
             <filter>pdf == True</filter>
         </data>
     </outputs>