# HG changeset patch
# User bgruening
# Date 1375711791 14400
# Node ID 21d563d5f2b291e2053ba235a13ab4874c3f2dd6
# Parent  09b65c12a75aa7ed424e43c88c5671952d7a9086
Uploaded

diff -r 09b65c12a75a -r 21d563d5f2b2 bamCompare.xml
--- a/bamCompare.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/bamCompare.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,12 +1,16 @@
 <tool id="bamCompare" name="bamCompare" version="1.0">
   <description>Normalize and compare two BAM files to output ratio, log2ratio or difference.</description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
   </requirements>
   <command>
   bamCompare
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --bamfile1 '$bamFile1'
   -bai1 '${bamFile1.metadata.bam_index}'
   --bamfile2 '$bamFile2'
@@ -28,8 +32,7 @@
   #end if
 
   --ratio $comparison.type
-  
-  
+
   #if $comparison.type=='subtract':
     #if $comparison.normalization.type=='rpkm':
       --normalizeUsingRPKM
@@ -37,27 +40,26 @@
       --normalizeTo1x $comparison.normalization.normalizeTo1x
     #end if
   #end if
-  
+
   #if $advancedOpt.showAdvancedOpt == "yes":
     #if $advancedOpt.smoothLength:
       --smoothLength '$advancedOpt.smoothLength'
     #end if
-    
+
     #if str($advancedOpt.region.value) != '':
       --region '$advancedOpt.region'
     #end if
+
     $advancedOpt.doNotExtendPairedEnds
     $advancedOpt.ignoreDuplicates
-    
+
     #if $advancedOpt.minMappingQuality:
       --minMappingQuality '$advancedOpt.minMappingQuality'
     #end if
-    
+
     --missingDataAsZero $advancedOpt.missingDataAsZero
-    
+
   #end if
-  --numberOfProcessors 4
-  
 
   </command>
 
@@ -76,7 +78,6 @@
        label="Bin size in bp"
        help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads)  will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
 
-
     <conditional name="scaling">
       <param name="method" type="select" 
          label="Method to use for scaling the largest sample to the smallest">
@@ -130,41 +131,40 @@
         <option value="bigwig" selected="true">bigwig</option>
     <option value="bedgraph">bedgraph</option>
     </param>
-    
-        <conditional name="advancedOpt">
-    <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-        <option value="no" selected="true">no</option>
-        <option value="yes">yes</option>
-      </param>
-      <when value="no" />
-      <when value="yes">
-    
-     <param name="smoothLength" type="integer" value="1" optional="true" min="1"
-       label="Smooth values using the following length (in bp)"
-       help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
+
+    <conditional name="advancedOpt">
+        <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+            <option value="no" selected="true">no</option>
+            <option value="yes">yes</option>
+        </param>
+        <when value="no" />
+        <when value="yes">
+
+        <param name="smoothLength" type="integer" value="1" optional="true" min="1"
+            label="Smooth values using the following length (in bp)"
+            help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
+
+        <param name="region" type="text" value=""
+            label="Region of the genome to limit the operation to"
+            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
 
-    <param name="region" type="text" value=""
-       label="Region of the genome to limit the operation to"
-       help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
-       
-     <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
-        label="Do not extend paired ends"
-        help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
-      
-     <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
-        label="Ignore duplicates"
-        help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 
-      
-      <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
-        label="Minimum mapping quality"
-        help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
-        
-      <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
-       label ="Treat missing data as zero"
-       help  ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
+        <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
+            label="Do not extend paired ends"
+            help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
+
+        <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
+            label="Ignore duplicates"
+            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 
 
-    </when>
- </conditional>
+        <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
+            label="Minimum mapping quality"
+            help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
+
+        <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
+            label ="Treat missing data as zero"
+            help  ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
+        </when>
+    </conditional>
 
   </inputs>
   <outputs>
diff -r 09b65c12a75a -r 21d563d5f2b2 bamCorrelate.xml
--- a/bamCorrelate.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/bamCorrelate.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,20 +1,36 @@
-<tool id="bamCorrelate" name="bamCorrelate" version="1.0">
+<tool id="bamCorrelate" name="bamCorrelate" version="1.0.1">
   <description>corrlates pairs of bam files</description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
   <command>
-  #set files=[]
-  #set labels=[]
-  #for $i in $inputs
-    #set $files += [str($i.bamfile)]
-    #if str($i.label.value) != "":
-        #set $labels += ["\"%s\"" % ($i.label.value)]
-    #else
-        #set $labels += ["\"%s\"" % ($i.bamfile.name)]
-    #end if
-  #end for
+    #import tempfile
+    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+
+    #set files=[]
+    #set labels=[]
+    #for $i in $inputs
+
+        #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
+        #set $temp_input_path = $temp_input_handle.name
+        #silent $temp_input_handle.close()
+        #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
+        #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
+        #silent $files.append('%s.bam' % $temp_input_path)
+
+
+        ##set $files += [str($i.bamfile)]
+        #if str($i.label.value) != "":
+            #set $labels += ["\"%s\"" % ($i.label.value)]
+        #else
+            #set $labels += ["\"%s\"" % ($i.bamfile.name)]
+        #end if
+    #end for
   bamCorrelate
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --bamfiles #echo " ".join($files)
   --labels #echo " ".join($labels)
   
@@ -25,12 +41,8 @@
   --plotFile $newoutFileName
   
   #if $outputOpt.showOutputOpt == "yes"
-      #if $outputOpt.outFileRawCounts:
-        --outRawCounts '$outputOpt.outFileRawCounts' 
-      #end if
-      #if $outputOpt.outFileCorMatrix:
-        --outFileCorMatrix '$outputOpt.outFileCorMatrix'
-      #end if
+        --outRawCounts '$outFileRawCounts' 
+        --outFileCorMatrix '$outFileCorMatrix'
   #end if
   
   #if $advancedOpt.showAdvancedOpt == "yes":
@@ -53,12 +65,11 @@
       --minMappingQuality '$advancedOpt.minMappingQuality'
     #end if
   #end if
-  
-  --numberOfProcessors 4; mv $newoutFileName $outFileName
+  ; mv $newoutFileName $outFileName
+  ; rm $temp_dir -rf
   </command>
 
   <inputs>
-  
   <repeat name="inputs" title="Input files" min="2">
     <param name="bamfile" type="data" format="bam" 
         label="Bam file" 
@@ -67,7 +78,7 @@
         label="Label"
         help="Label to use in the output. If not given the dataset name will be used instead."/>
   </repeat>
-  
+
   <param name="fragmentLength" type="integer" value="300" min="1"
        label="Length of the average fragment size"
        help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
diff -r 09b65c12a75a -r 21d563d5f2b2 bamCoverage.xml
--- a/bamCoverage.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/bamCoverage.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,11 +1,16 @@
 <tool id="bamCoverage" name="bamCoverage" version="1.0">
   <description>Given a BAM file, generates a coverage bigwig file.  Multiple options available to count reads and normalize coverage.</description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
   </requirements>
-  <command>bamCoverage
+  <command>
+  bamCoverage
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --bam '$bamInput'
   --bamIndex ${bamInput.metadata.bam_index}
   --outFileName '$outFileName'
@@ -13,7 +18,6 @@
 
   --fragmentLength $fragmentLength
   --binSize $binSize
-  
 
   #if $scaling.type=='rpkm':
     --normalizeUsingRPKM
@@ -27,19 +31,18 @@
     #if $advancedOpt.smoothLength:
       --smoothLength '$advancedOpt.smoothLength'
     #end if
-    
+
     #if str($advancedOpt.region.value) != '':
       --region '$advancedOpt.region'
     #end if
     $advancedOpt.doNotExtendPairedEnds
     $advancedOpt.ignoreDuplicates
-    
+
     #if $advancedOpt.minMappingQuality:
       --minMappingQuality '$advancedOpt.minMappingQuality'
     #end if
-    
+
   #end if
-  --numberOfProcessors 4
   </command>
 
   <inputs>
@@ -64,59 +67,56 @@
       <when value="rpkm"/>
       <when value="no"/>
       <when value="1x">
-    <param name="normalizeTo1x" type="integer" value="2150570000"
+        <param name="normalizeTo1x" type="integer" value="2150570000"
            label="Genome size"
            help ="Enter the genome size to normalize the reads counts. Sequencing depth is defined as the total number of mapped reads * fragment length / effective genome size. To use this option, the effective genome size has to be given. Common values are: mm9: 2150570000, hg19:2451960000, dm3:121400000 and ce10:93260000."/>
       </when>
       <when value="own">
-    <param name="scaleFactor" type="float" value="1" size="3" 
+        <param name="scaleFactor" type="float" value="1" size="3" 
            label="Scale factor to multiply all values" />
-      </when>
+        </when>
     </conditional>
 
     <param name="outFileFormat" type="select" label="Coverage file format">
         <option value="bigwig" selected="true">bigwig</option>
-    <option value="bedgraph">bedgraph</option>
+        <option value="bedgraph">bedgraph</option>
     </param>
-    
-    
+
     <conditional name="advancedOpt">
-    <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-        <option value="no" selected="true">no</option>
-        <option value="yes">yes</option>
-      </param>
+        <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+            <option value="no" selected="true">no</option>
+            <option value="yes">yes</option>
+        </param>
       <when value="no" />
       <when value="yes">
-    
-     <param name="smoothLength" type="integer" value="1" optional="true" min="1"
-       label="Smooth values using the following length (in bp)"
-       help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
+         <param name="smoothLength" type="integer" value="1" optional="true" min="1"
+           label="Smooth values using the following length (in bp)"
+           help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
+
+        <param name="region" type="text" value=""
+           label="Region of the genome to limit the operation to"
+           help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
 
-    <param name="region" type="text" value=""
-       label="Region of the genome to limit the operation to"
-       help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
-       
-     <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
-        label="Do not extend paired ends"
-        help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
-      
-     <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
-        label="Ignore duplicates"
-        help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 
-      
-      <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
-        label="Minimum mapping quality"
-        help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
-    </when>
- </conditional>
+         <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
+            label="Do not extend paired ends"
+            help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
 
+         <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
+            label="Ignore duplicates"
+            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." /> 
+
+          <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
+            label="Minimum mapping quality"
+            help= "If set, only reads that have a mapping quality score higher than the given value are considered"/>
+        </when>
+    </conditional>
   </inputs>
   <outputs>
     <data format="bigwig" name="outFileName">
-    <change_format>
-        <when input="outFileFormat" value="bigwig" format="bigwig" />
-        <when input="outFileFormat" value="bedgraph" format="bedgraph" />
-    </change_format>
+        <change_format>
+            <when input="outFileFormat" value="bigwig" format="bigwig" />
+            <when input="outFileFormat" value="bedgraph" format="bedgraph" />
+        </change_format>
     </data>
   </outputs>
   <help>
@@ -139,5 +139,4 @@
 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
 
 </help>
-  
 </tool>
diff -r 09b65c12a75a -r 21d563d5f2b2 bamFingerprint.xml
--- a/bamFingerprint.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/bamFingerprint.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,60 +1,74 @@
 <tool id="bamFingerprint" name="bamFingerprint" version="1.0">
   <description>plots profiles of bam files</description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
   <command>
-  #set files=[]
-  #set labels=[]
-  #for $i in $inputs
-    #set $files += [str($i.bamfile)]
-    #if str($i.label.value) != "":
-        #set $labels += ["\"%s\"" % ($i.label.value)]
-    #else
-        #set $labels += ["\"%s\"" % ($i.bamfile.name)]
-    #end if
-  #end for
+    #import tempfile
+    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+
+    #set files=[]
+    #set labels=[]
+    #for $i in $inputs
+        #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
+        #set $temp_input_path = $temp_input_handle.name
+        #silent $temp_input_handle.close()
+        #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
+        #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
+        #silent $files.append('%s.bam' % $temp_input_path)
+
+        ##set $files += [str($i.bamfile)]
+        #if str($i.label.value) != "":
+            #set $labels += ["\"%s\"" % ($i.label.value)]
+        #else
+            #set $labels += ["\"%s\"" % ($i.bamfile.name)]
+        #end if
+    #end for
+
   bamFingerprint
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --bamfiles #echo " ".join($files)
   --labels #echo " ".join($labels)
-  
+
   --fragmentLength $fragmentLength
-  
+
   #set newoutFileName=str($outFileName)+".png"
   --plotFile $newoutFileName
-  
+
   #if $outputOpt.showOutputOpt == "yes"
       #if $outputOpt.saveRawCounts:
         --outRawCounts '$outFileRawCounts' 
       #end if
   #end if
-  
+
   #if $advancedOpt.showAdvancedOpt == "yes":
     #if $advancedOpt.smoothLength:
       --smoothLength '$advancedOpt.smoothLength'
     #end if
-    
+
     #if str($advancedOpt.region.value) != '':
       --region '$advancedOpt.region'
     #end if
-    
+
     --binSize '$advancedOpt.binSize'
     --numberOfSamples '$advancedOpt.numberOfSamples'
-    
+
     $advancedOpt.doNotExtendPairedEnds
     $advancedOpt.ignoreDuplicates
     $advancedOpt.skipZeros
-    
+
     #if $advancedOpt.minMappingQuality:
       --minMappingQuality '$advancedOpt.minMappingQuality'
     #end if
   #end if
-  
-  --numberOfProcessors 4; mv $newoutFileName $outFileName
+  ; mv $newoutFileName $outFileName
+  ; rm $temp_dir -rf
   </command>
 
   <inputs>
-  
   <repeat name="inputs" title="Input files" min="2">
     <param name="bamfile" type="data" format="bam" 
         label="Bam file" 
@@ -63,10 +77,8 @@
         label="Label"
         help="Label to use in the output. If not given the dataset name will be used instead."/>
   </repeat>
-  
   <param name="fragmentLength" type="integer" value="200" min="1"
        label="Length of the average fragment size"/>
-  
   <conditional name="advancedOpt">
     <param name="showAdvancedOpt" type="select" label="Show advanced options" >
       <option value="no" selected="true">no</option>
diff -r 09b65c12a75a -r 21d563d5f2b2 bigwigCompare.xml
--- a/bigwigCompare.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/bigwigCompare.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,12 +1,16 @@
 <tool id="bigwigCompare" name="bigwigCompare" version="1.0">
   <description>compares two bigwig files based on the number of mapped reads</description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
     <requirement type="package" version="1.7.1">numpy</requirement>
   </requirements>
   <command>
   bigwigCompare
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --bigwig1 '$bigwigFile1'
   --bigwig2 '$bigwigFile2'
 
@@ -14,26 +18,22 @@
   --outFileFormat '$outFileFormat'
 
   --ratio $comparison_type
-  
-  #if $advancedOpt.showAdvancedOpt == "yes":
-    #if str($advancedOpt.region.value) != '':
-      --region '$advancedOpt.region'
+
+    #if $advancedOpt.showAdvancedOpt == "yes":
+      #if str($advancedOpt.region.value) != '':
+        --region '$advancedOpt.region'
+      #end if
+
+      --missingDataAsZero $advancedOpt.missingDataAsZero
+      --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
+      --pseudocount '$advancedOpt.pseudocount'
+      --binSize $advancedOpt.binSize
+
     #end if
-  
-    --missingDataAsZero $advancedOpt.missingDataAsZero
-    --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
-    --pseudocount '$advancedOpt.pseudocount'
-    --binSize $advancedOpt.binSize
-    
-  #end if
-  --numberOfProcessors 4
-  
 
   </command>
-
   <inputs>
     <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
-
     <param name="bigwigFile2" format="bigwig" type="data" label="Input bigwig file" />
 
       <param name="comparison_type" type="select" 
@@ -48,36 +48,33 @@
 
     <param name="outFileFormat" type="select" label="Coverage file format">
         <option value="bigwig" selected="true">bigwig</option>
-    <option value="bedgraph">bedgraph</option>
+        <option value="bedgraph">bedgraph</option>
     </param>
-    
-        <conditional name="advancedOpt">
-    <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-        <option value="no" selected="true">no</option>
-        <option value="yes">yes</option>
-      </param>
-      <when value="no" />
-      <when value="yes">
-      
-          <param name="binSize" type="integer" value="50" min="1" 
-       label="Bin size in bp"
-       help="Size of the bins in bp for the ouput of the bigwig/bedgraph file "/>
-    
-    <param name="region" type="text" value=""
-       label="Region of the genome to limit the operation to"
-       help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
-       
-    <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
-       label ="Treat missing data as zero"
-       help  ="This parameter determines if missing data should be replaced with a zero. If set to &quot;no&quot;, missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage." />
-    
-    <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment"/>
-    <param name="scaleFactor2" type="float" value="1" label="Scale factor for input"/>
-    <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+
+    <conditional name="advancedOpt">
+        <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+            <option value="no" selected="true">no</option>
+            <option value="yes">yes</option>
+        </param>
+        <when value="no" />
+        <when value="yes">
+            <param name="binSize" type="integer" value="50" min="1" 
+                label="Bin size in bp"
+                help="Size of the bins in bp for the ouput of the bigwig/bedgraph file "/>
 
-    </when>
- </conditional>
+            <param name="region" type="text" value=""
+                label="Region of the genome to limit the operation to"
+                help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
 
+            <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
+                label ="Treat missing data as zero"
+                help  ="This parameter determines if missing data should be replaced with a zero. If set to &quot;no&quot;, missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage." />
+
+            <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment"/>
+            <param name="scaleFactor2" type="float" value="1" label="Scale factor for input"/>
+            <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+        </when>
+    </conditional>
   </inputs>
   <outputs>
     <data format="bigwig" name="outFileName">
diff -r 09b65c12a75a -r 21d563d5f2b2 computeGCBias.xml
--- a/computeGCBias.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/computeGCBias.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,24 +1,37 @@
-<tool id="computeGCBias" name="computeGCBias" version="1.0">
+<tool id="computeGCBias" name="computeGCBias" version="1.0.1">
   <description></description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
   <stdio>
     <exit_code range="0" level="warning" description="Warning" />
   </stdio>
   <command>
+    #import tempfile
+    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+
+    #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
+    #set $temp_bam_path = $temp_bam_handle.name + '.bam'
+    #silent $temp_bam_handle.close()
+    #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
+    #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
+
   computeGCBias
-  --bamfile '$bamInput'
+
+  ##ToDo
+  --numberOfProcessors 4
+
+  --bamfile '$temp_bam_path'
   --species '$species'
   --GCbiasFrequenciesFile $outFileName
   --fragmentLength $fragmentLength
-  
+
   #if $source.ref_source=="history":
     --genome $source.input1
   #else:
     --genome "${source.input1_2bit.fields.path}"
   #end if
-  
+
   #if $advancedOpt.showAdvancedOpt == "yes":
     #if str($advancedOpt.region.value) != '':
       --region '$advancedOpt.region'
@@ -27,60 +40,65 @@
     --binSize '$advancedOpt.binSize'
     --sampleSize '$advancedOpt.sampleSize'
     --regionSize '$advancedOpt.regionSize'
-    
+
     #if $advancedOpt.filterOut:
       --filterOut $advancedOpt.filterOut
     #end if
-    
+
     #if $advancedOpt.extraSampling:
       --extraSampling $advancedOpt.extraSampling
     #end if
-    
+
   #end if
-  
-  #set move=""
+
   #if $output.showOutputSettings == "yes"
       #if $output.saveBiasPlot:
-        --biasPlot biasPlot.png
-        #set move="mv biasPlot.png $biasPlot"
+        --biasPlot biasPlot.png ;
+        mv biasPlot.png $biasPlot
       #end if
   #end if
-  ; $move
+
+  ; rm $temp_dir -rf
 
   </command>
+  <inputs>
 
-  <inputs>
-  
-  <param name="bamInput" format="bam" type="data" label="Input BAM file"
-       help="The BAM file must be sorted and indexed."/>
-  
-  <param name="species" type="text" value="" label="Species name abbreviation" />
-  
-  <conditional name="source">
-    <param name="ref_source" type="select" label="Reference genome">
-        <option value="cached">locally cached</option>
-        <option value="history">in your history</option>
-    </param>
-    <when value="cached">
-        <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
-            <options from_data_table="deepTools_seqs" />
+      <param name="bamInput" format="bam" type="data" label="Input BAM file"
+        help="The BAM file must be sorted and indexed."/>
+      <!--<param name="species" type="text" value="" label="Species name abbreviation" />-->
+
+        <param name="species" type="select" label="Species name abbreviation">
+            <option value="hg19">hg19</option>
+            <option value="ce10">ce10</option>
+            <option value="dm3">dm3</option>
+            <option value="mm9">mm9</option>
+        </param>
+
+      <conditional name="source">
+        <param name="ref_source" type="select" label="Reference genome">
+            <option value="cached">locally cached</option>
+            <option value="history">in your history</option>
         </param>
-    </when>
-    <when value="history">
-        <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
-    </when>
-  </conditional>
-  <param name="fragmentLength" type="integer" value="300" min="1"
-     label="Fragment length used for the sequencing"
-     help ="If paired-end reads are used the fragment length is computed based from the bam file."/>
-  
-  <conditional name="advancedOpt">
-    <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-        <option value="no" selected="true">no</option>
-        <option value="yes">yes</option>
-      </param>
-      <when value="no" />
-      <when value="yes">
+        <when value="cached">
+            <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+                <options from_data_table="deepTools_seqs" />
+            </param>
+        </when>
+        <when value="history">
+            <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
+        </when>
+      </conditional>
+      <param name="fragmentLength" type="integer" value="300" min="1"
+        label="Fragment length used for the sequencing"
+        help ="If paired-end reads are used the fragment length is computed based from the bam file."/>
+
+    <conditional name="advancedOpt">
+        <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+            <option value="no" selected="true">no</option>
+            <option value="yes">yes</option>
+        </param>
+        <when value="no" />
+        <when value="yes">
           <param name="region" type="text" value=""
             label="Region of the genome to limit the operation to"
             help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
@@ -102,10 +120,10 @@
            <param name="extraSampling" type="data" format="bed" optional="true"
              label="BED file containing genomic regions for which extra sampling is required because they are underrepresented in the genome"
              help="" />
-      </when>
-  </conditional>
+        </when>
+    </conditional>
 
-  <conditional name="output" >
+    <conditional name="output" >
         <param name="showOutputSettings" type="select" label="Show additional output options" >
         <option value="no" selected="true">no</option>
         <option value="yes">yes</option>
@@ -143,5 +161,4 @@
 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
 
   </help>
-  
 </tool>
diff -r 09b65c12a75a -r 21d563d5f2b2 computeMatrix.xml
--- a/computeMatrix.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/computeMatrix.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,15 +1,19 @@
 <tool id="computeMatrix" name="computeMatrix" version="1.0">
   <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
   <command>
   computeMatrix
+
+  ##ToDo
+  --numberOfProcessors 4
+
   $mode.mode_select
   --regionsFileName '$regionsFile'
   --scoreFileName '$scoreFile'
   --outFileName '$outFileName'
-  
+
   #if $output.showOutputSettings == "yes"
       #if $output.saveData:
         --outFileNameData '$outFileNameData' 
@@ -17,12 +21,12 @@
       #if $output.saveMatrix:
       --outFileNameMatrix '$outFileNameMatrix'
       #end if
-      
+
       #if $output.saveSortedRegions:
         --outFileSortedRegions '$outFileSortedRegions'
       #end if
   #end if
-  
+
   #if $mode.mode_select == "reference-point":
     --referencePoint $mode.referencePoint
     $mode.nanAfterEnd
@@ -37,15 +41,15 @@
       --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
     #end if
   #end if
-  
+
   #if $advancedOpt.showAdvancedOpt == "yes":
     --sortRegions '$advancedOpt.sortRegions'
     --sortUsing '$advancedOpt.sortUsing'
     --averageTypeBins '$advancedOpt.averageTypeBins'
     $advancedOpt.missingDataAsZero
     $advancedOpt.skipZeros
-    -bs $advancedOpt.binSize
-    
+    --binSize $advancedOpt.binSize
+
     #if $advancedOpt.minThreshold:
     --minThreshold $advancedOpt.minThreshold
     #end if
@@ -55,20 +59,20 @@
     #if $advancedOpt.scale:
     --scale $advancedOpt.scale
     #end if
-  
+
   #end if
-  --numberOfProcessors 4
+
   </command>
   <inputs>
     <param name="regionsFile" format="bed,gff" type="data" label="Regions to plot" help="File, in BED or GFF format, containing the regions to plot."/>
     <param name="scoreFile" format="bigwig,bam" type="data" label="Score file" help="Either a bigWig file (containing a score, usually covering the whole genome) or a BAM file. For this last case, coverage counts will be used for the heatmap."/>
-    
+
     <conditional name="mode" >
       <param name="mode_select" type="select" label="computeMatrix has two main output options" help="In the scale-regions mode, all regions in the BED/GFF file are stretched or shrunk to the same length (bp) that is indicated by the user. Reference-point refers to a position within the BED/GFF regions (e.g start of region). In the reference-point mode only those genomic positions before (downstream) and/or after (upstream) the reference point will be plotted.">
         <option value="scale-regions" selected="true">scale-regions</option>
         <option value="reference-point">reference-point</option>
       </param>
-      
+
       <when value="scale-regions" >
         <param name="regionBodyLength" type="integer" value="500" label="Distance in bp to which all regions are going to be fitted"/>
         <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" help ="Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
@@ -112,8 +116,7 @@
         <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
     </when>
     </conditional>
-    
-    
+
     <conditional name="advancedOpt" >
       <param name="showAdvancedOpt" type="select" label="Show advanced options" >
         <option value="no" selected="true">no</option>
@@ -121,16 +124,14 @@
       </param>
       <when value="no" />
       <when value="yes">
-        
         <param name="binSize" type="integer" value="100" min="1" optional="true" label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length" />
-        
         <param name="sortRegions" type="select" label="Sort regions"
            help="Whether the output file should present the regions sorted.">
           <option value="no" selected="true">no ordering</option>
           <option value="descend">descending order</option>
           <option value="ascend">ascending order</option>
         </param>
-        
+
         <param name="sortUsing" type="select" label="Method used for sorting." help="The value is computed for each row." >
           <option value="mean" selected="true">mean</option>
           <option value="median">median</option>
@@ -139,7 +140,7 @@
           <option value="sum">sum</option>
           <option value="region_length">region length</option>
         </param>
-        
+
         <param name="averageTypeBins" type="select" label="Define the type of statistic that should be used over the bin size range">
           <option value="mean" selected="true">mean</option>
           <option value="median">median</option>
@@ -148,11 +149,9 @@
           <option value="sum">sum</option>
           <option value="std">std</option>
         </param>
-        
+
         <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue="" label="Indicate missing data as zero" help="Only for bigwig input! Set to &quot;yes&quot;, if missing data should be indicated as zeros. Default is to ignore such cases which will be depicted as black areas in the heatmap. (see &quot;Missing data color&quot; options of the heatmapper for additional options)."/>
-        
         <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue="" label="Skip zeros" help="Whether regions with only scores of zero should be included or not. Default is to include them."/>
-        
         <param name="minThreshold" type="float" optional="true" label="Minimum threshold" help="Any region containing a value that is equal or less than this numeric value will be skipped. This is useful to skip, for example, genes where the read count is zero for any of the bins. This could be the result of unmappable areas and can bias the overall results."/>
         <param name="maxThreshold" type="float" optional="true" label="Maximum threshold" help="Any region containing a value that is equal or higher that this numeric value will be skipped. The max threshold is useful to skip those few regions with very high read counts (e.g. major satellites) that may bias the average values."/>
         <param name="scale" type="float" optional="true" label="Scale" help="If set, all values are multiplied by this number."/>
@@ -204,5 +203,4 @@
 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
   </help>
-
 </tool>
diff -r 09b65c12a75a -r 21d563d5f2b2 correctGCBias.xml
--- a/correctGCBias.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/correctGCBias.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,13 +1,23 @@
-<tool id="correctGCBias" name="correctGCBias" version="1.0">
+<tool id="correctGCBias" name="correctGCBias" version="1.0.1">
   <description>
   </description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
   </requirements>
   <command>
+    #import tempfile
+    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+
+    #set $temp_bam_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
+    #set $temp_bam_path = $temp_bam_handle.name + '.bam'
+    #silent $temp_bam_handle.close()
+    #silent os.system("ln -s %s %s" % (str($bamInput), $temp_bam_path))
+    #silent os.system("ln -s %s %s.bai" % (str($bamInput.metadata.bam_index), $temp_bam_path))
+
+
   correctGCBias
-  --bamfile '$bamInput'
+  --bamfile '$temp_bam_path'
   --species '$species'
   --GCbiasFrequenciesFile $GCbiasFrequenciesFile
   
@@ -32,13 +42,18 @@
   </command>
 
   <inputs>
-  
+
   <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
-  
+
   <param name="bamInput" format="bam" type="data" label="Input BAM file" help="The BAM file must be sorted and indexed."/>
-  
-  <param name="species" type="text" value="" label="Species name abbreviation" />
-  
+
+  <param name="species" type="select" label="Species name abbreviation">
+    <option value="hg19">hg19</option>
+    <option value="ce10">ce10</option>
+    <option value="dm3">dm3</option>
+    <option value="mm9">mm9</option>
+  </param>
+
   <conditional name="source">
     <param name="ref_source" type="select" label="Reference genome">
         <option value="cached">locally cached</option>
diff -r 09b65c12a75a -r 21d563d5f2b2 heatmapper.xml
--- a/heatmapper.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/heatmapper.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -7,23 +7,27 @@
     <requirement type="package" version="1.2.1">matplotlib</requirement>
     <requirement type="package" version="0.12.0">scipy</requirement>
     <requirement type="package" version="0.1">ucsc_tools</requirement>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
 
   <command>
   heatmapper
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --matrixFile $matrixFile
   #if $output.showOutputSettings == "yes"
       #set newoutFileName=str($outFileName)+"."+str($output.outFileFormat)
       --outFileName $newoutFileName
       #if $outFileNameData:
-        --outFileNameData '$outFileNameData' 
+        --outFileNameData '$outFileNameData'
       #end if
 
       #if $outFileNameMatrix:
       --outFileNameMatrix '$outFileNameMatrix'
       #end if
-      
+
       #if $outFileSortedRegions:
         --outFileSortedRegions '$outFileSortedRegions'
       #end if
@@ -34,61 +38,61 @@
   
   #if $advancedOpt.showAdvancedOpt == "yes"
       #if $advancedOpt.sortRegions:
-      --sortRegions '$advancedOpt.sortRegions'
+        --sortRegions '$advancedOpt.sortRegions'
       #end if
       
       #if $advancedOpt.sortUsing:
-      --sortUsing '$advancedOpt.sortUsing'
+        --sortUsing '$advancedOpt.sortUsing'
       #end if
       
       #if $advancedOpt.averageTypeSummaryPlot:
-      --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
+        --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
       #end if
       
       #if str($advancedOpt.missingDataColor.value) != "None":
-      --missingDataColor '$advancedOpt.missingDataColor'
+        --missingDataColor '$advancedOpt.missingDataColor'
       #end if
       
       --colorMap '$advancedOpt.colorMap'
       
       #if $advancedOpt.zMin:
-      --zMin $advancedOpt.zMin
+        --zMin $advancedOpt.zMin
       #end if
       #if $advancedOpt.zMax:
-      --zMax $advancedOpt.zMax
+        --zMax $advancedOpt.zMax
       #end if
       
       #if $advancedOpt.yMin:
-      --yMin $advancedOpt.yMin
+        --yMin $advancedOpt.yMin
       #end if
       #if $advancedOpt.yMax:
-      --yMax $advancedOpt.yMax
+        --yMax $advancedOpt.yMax
       #end if
-      
+
       --xAxisLabel '$advancedOpt.xAxisLabel'
       --yAxisLabel '$advancedOpt.yAxisLabel'
-      
+
       --heatmapWidth $advancedOpt.heatmapWidth
       --heatmapHeight $advancedOpt.heatmapHeight
-      
+
       --whatToShow '$advancedOpt.whatToShow'
-      
+
       --startLabel '$advancedOpt.startLabel' 
       --endLabel '$advancedOpt.endLabel'
       --refPointLabel '$advancedOpt.referencePointLabel'
       --regionsLabel '$advancedOpt.regionsLabel'
-      
+
       #if str($advancedOpt.plotTitle.value) != "None":
       --plotTitle '$advancedOpt.plotTitle'
       #end if
-      
+
       $advancedOpt.onePlotPerGroup
   #end if
+
   ; mv $newoutFileName $outFileName
   </command>
   <inputs>
     <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
-    
     <conditional name="output" >
         <param name="showOutputSettings" type="select" label="Show advanced output settings" >
         <option value="no" selected="true">no</option>
@@ -108,7 +112,7 @@
         <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
     </when>
     </conditional>
-    
+
     <conditional name="advancedOpt" >
       <param name="showAdvancedOpt" type="select" label="Show advanced options" >
         <option value="no" selected="true">no</option>
@@ -122,7 +126,7 @@
           <option value="descend">descending order</option>
           <option value="ascend">ascending order</option>
         </param>
-        
+
         <param name="sortUsing" type="select" label="Method used for sorting" help="For each row the method is computed." >
           <option value="mean" selected="true">mean</option>
           <option value="median">median</option>
@@ -131,7 +135,7 @@
           <option value="sum">sum</option>
           <option value="region_length">region length</option>
         </param>
-        
+
         <param name="averageTypeSummaryPlot" type="select" label="Type of statistic that should be plotted in the summary image above the heatmap">
           <option value="mean" selected="true">mean</option>
           <option value="median">median</option>
@@ -140,163 +144,161 @@
           <option value="sum">sum</option>
           <option value="std">std</option>
         </param>
-        
+
         <param name="missingDataColor" type="text" label="Missing data color" value="black" optional="true" help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default. By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0). Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html. Alternatively colors can be specified using the #rrggbb notation." />
-        
+
         <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available values can be seen here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
-        <option value="RdYlBu" selected="true">RdYlBu</option>
-        <option value="Accent">Accent</option>
-        <option value="Spectral">Spectral</option>
-        <option value="Set1">Set1</option>
-        <option value="Set2">Set2</option>
-        <option value="Set3">Set3</option>
-        <option value="Dark2">Dark2</option>
-        <option value="Reds">Reds</option>
-        <option value="Oranges">Oranges</option>
-        <option value="Greens">Greens</option>
-        <option value="Blues">Blues</option>
-        <option value="Greys">Greys</option>
-        <option value="Purples">Purples</option>
-        <option value="Paired">Paired</option>
-        <option value="Pastel1">Pastel1</option>
-        <option value="Pastel2">Pastel2</option>
-        <option value="spring">spring</option>
-        <option value="summer">summer</option>
-        <option value="autumn">autumn</option>
-        <option value="winter">winter</option>
-        <option value="hot">hot</option>
-        <option value="coolwarm">coolwarm</option>
-        <option value="cool">cool</option>
-        <option value="seismic">seismic</option>
-        <option value="terrain">terrain</option>
-        <option value="ocean">ocean</option>
-        <option value="rainbow">rainbow</option>
-        <option value="bone">bone</option>
-        <option value="flag">flag</option>
-        <option value="prism">prism</option>
-        <option value="cubehelix">cubehelix</option>
-        <option value="binary">binary</option>
-        <option value="pink">pink</option>
-        <option value="gray">gray</option>
-        <option value="copper">copper</option>
-        <option value="BrBG">BrBG</option>
-        <option value="BuGn">BuGn</option>
-        <option value="BuPu">BuPu</option>
-        <option value="GnBu">GnBu</option>
-        <option value="OrRd">OrRd</option>
-        <option value="PiYG">PiYG</option>
-        <option value="PRGn">PRGn</option>
-        <option value="PuOr">PuOr</option>
-        <option value="PuRd">PuRd</option>
-        <option value="PuBu">PuBu</option>
-        <option value="RdBu">RdBu</option>
-        <option value="RdGy">RdGy</option>
-        <option value="RdPu">RdPu</option>
-        <option value="YlGn">YlGn</option>
-        <option value="PuBuGn">PuBuGn</option>
-        <option value="RdYlGn">RdYlGn</option>
-        <option value="YlGnBu">YlGnBu</option>
-        <option value="YlOrBr">YlOrBr</option>
-        <option value="YlOrRd">YlOrRd</option>
-        <option value="gist_gray">gist_gray</option>
-        <option value="gist_stern">gist_stern</option>
-        <option value="gist_earth">gist_earth</option>
-        <option value="gist_yarg">gist_yarg</option>
-        <option value="gist_ncar">gist_ncar</option>
-        <option value="gist_rainbow">gist_rainbow</option>
-        <option value="gist_heat">gist_heat</option>
-        <option value="gnuplot">gnuplot</option>
-        <option value="gnuplot2">gnuplot2</option>
-        <option value="CMRmap">CMRmap</option>
-        <option value="bwr">bwr</option>
-        <option value="hsv">hsv</option>
-        <option value="brg">brg</option>
-        <option value="jet">jet</option>
-        <option value="afmhot">afmhot</option>
-        
-        <option value="Accent_r">Accent reversed</option>
-        <option value="Spectral_r">Spectral reversed</option>
-        <option value="Set1_r">Set1 reversed</option>
-        <option value="Set2_r">Set2 reversed</option>
-        <option value="Set3_r">Set3 reversed</option>
-        <option value="Dark2_r">Dark2 reversed</option>
-        <option value="Reds_r">Reds reversed</option>
-        <option value="Oranges_r">Oranges reversed</option>
-        <option value="Greens_r">Greens reversed</option>
-        <option value="Blues_r">Blues reversed</option>
-        <option value="Greys_r">Greys reversed</option>
-        <option value="Purples_r">Purples reversed</option>
-        <option value="Paired_r">Paired reversed</option>
-        <option value="Pastel1_r">Pastel1 reversed</option>
-        <option value="Pastel2_r">Pastel2 reversed</option>
-        <option value="spring_r">spring reversed</option>
-        <option value="summer_r">summer reversed</option>
-        <option value="autumn_r">autumn reversed</option>
-        <option value="winter_r">winter reversed</option>
-        <option value="hot_r">hot reversed</option>
-        <option value="coolwarm_r">coolwarm reversed</option>
-        <option value="cool_r">cool reversed</option>
-        <option value="seismic_r">seismic reversed</option>
-        <option value="terrain_r">terrain reversed</option>
-        <option value="ocean_r">ocean reversed</option>
-        <option value="rainbow_r">rainbow reversed</option>
-        <option value="bone_r">bone reversed</option>
-        <option value="flag_r">flag reversed</option>
-        <option value="prism_r">prism reversed</option>
-        <option value="cubehelix_r">cubehelix reversed</option>
-        <option value="binary_r">binary reversed</option>
-        <option value="pink_r">pink reversed</option>
-        <option value="gray_r">gray reversed</option>
-        <option value="copper_r">copper reversed</option>
-        <option value="BrBG_r">BrBG reversed</option>
-        <option value="BuGn_r">BuGn reversed</option>
-        <option value="BuPu_r">BuPu reversed</option>
-        <option value="GnBu_r">GnBu reversed</option>
-        <option value="OrRd_r">OrRd reversed</option>
-        <option value="PiYG_r">PiYG reversed</option>
-        <option value="PRGn_r">PRGn reversed</option>
-        <option value="PuOr_r">PuOr reversed</option>
-        <option value="PuRd_r">PuRd reversed</option>
-        <option value="PuBu_r">PuBu reversed</option>
-        <option value="RdBu_r">RdBu reversed</option>
-        <option value="RdGy_r">RdGy reversed</option>
-        <option value="RdPu_r">RdPu reversed</option>
-        <option value="YlGn_r">YlGn reversed</option>
-        <option value="PuBuGn_r">PuBuGn reversed</option>
-        <option value="RdYlBu_r">RdYlBu reversed</option>
-        <option value="RdYlGn_r">RdYlGn reversed</option>
-        <option value="YlGnBu_r">YlGnBu reversed</option>
-        <option value="YlOrBr_r">YlOrBr reversed</option>
-        <option value="YlOrRd_r">YlOrRd reversed</option>
-        <option value="gist_gray_r">gist_gray reversed</option>
-        <option value="gist_stern_r">gist_stern reversed</option>
-        <option value="gist_earth_r">gist_earth reversed</option>
-        <option value="gist_yarg_r">gist_yarg reversed</option>
-        <option value="gist_ncar_r">gist_ncar reversed</option>
-        <option value="gist_rainbow_r">gist_rainbow reversed</option>
-        <option value="gist_heat_r">gist_heat reversed</option>
-        <option value="gnuplot_r">gnuplot reversed</option>
-        <option value="gnuplot2_r">gnuplot2 reversed</option>
-        <option value="CMRmap_r">CMRmap reversed</option>
-        <option value="bwr_r">bwr reversed</option>
-        <option value="hsv_r">hsv reversed</option>
-        <option value="brg_r">brg reversed</option>
-        <option value="jet_r">jet reversed</option>
-        <option value="afmhot_r">afmhot reversed</option>
+            <option value="RdYlBu" selected="true">RdYlBu</option>
+            <option value="Accent">Accent</option>
+            <option value="Spectral">Spectral</option>
+            <option value="Set1">Set1</option>
+            <option value="Set2">Set2</option>
+            <option value="Set3">Set3</option>
+            <option value="Dark2">Dark2</option>
+            <option value="Reds">Reds</option>
+            <option value="Oranges">Oranges</option>
+            <option value="Greens">Greens</option>
+            <option value="Blues">Blues</option>
+            <option value="Greys">Greys</option>
+            <option value="Purples">Purples</option>
+            <option value="Paired">Paired</option>
+            <option value="Pastel1">Pastel1</option>
+            <option value="Pastel2">Pastel2</option>
+            <option value="spring">spring</option>
+            <option value="summer">summer</option>
+            <option value="autumn">autumn</option>
+            <option value="winter">winter</option>
+            <option value="hot">hot</option>
+            <option value="coolwarm">coolwarm</option>
+            <option value="cool">cool</option>
+            <option value="seismic">seismic</option>
+            <option value="terrain">terrain</option>
+            <option value="ocean">ocean</option>
+            <option value="rainbow">rainbow</option>
+            <option value="bone">bone</option>
+            <option value="flag">flag</option>
+            <option value="prism">prism</option>
+            <option value="cubehelix">cubehelix</option>
+            <option value="binary">binary</option>
+            <option value="pink">pink</option>
+            <option value="gray">gray</option>
+            <option value="copper">copper</option>
+            <option value="BrBG">BrBG</option>
+            <option value="BuGn">BuGn</option>
+            <option value="BuPu">BuPu</option>
+            <option value="GnBu">GnBu</option>
+            <option value="OrRd">OrRd</option>
+            <option value="PiYG">PiYG</option>
+            <option value="PRGn">PRGn</option>
+            <option value="PuOr">PuOr</option>
+            <option value="PuRd">PuRd</option>
+            <option value="PuBu">PuBu</option>
+            <option value="RdBu">RdBu</option>
+            <option value="RdGy">RdGy</option>
+            <option value="RdPu">RdPu</option>
+            <option value="YlGn">YlGn</option>
+            <option value="PuBuGn">PuBuGn</option>
+            <option value="RdYlGn">RdYlGn</option>
+            <option value="YlGnBu">YlGnBu</option>
+            <option value="YlOrBr">YlOrBr</option>
+            <option value="YlOrRd">YlOrRd</option>
+            <option value="gist_gray">gist_gray</option>
+            <option value="gist_stern">gist_stern</option>
+            <option value="gist_earth">gist_earth</option>
+            <option value="gist_yarg">gist_yarg</option>
+            <option value="gist_ncar">gist_ncar</option>
+            <option value="gist_rainbow">gist_rainbow</option>
+            <option value="gist_heat">gist_heat</option>
+            <option value="gnuplot">gnuplot</option>
+            <option value="gnuplot2">gnuplot2</option>
+            <option value="CMRmap">CMRmap</option>
+            <option value="bwr">bwr</option>
+            <option value="hsv">hsv</option>
+            <option value="brg">brg</option>
+            <option value="jet">jet</option>
+            <option value="afmhot">afmhot</option>
+            <option value="Accent_r">Accent reversed</option>
+            <option value="Spectral_r">Spectral reversed</option>
+            <option value="Set1_r">Set1 reversed</option>
+            <option value="Set2_r">Set2 reversed</option>
+            <option value="Set3_r">Set3 reversed</option>
+            <option value="Dark2_r">Dark2 reversed</option>
+            <option value="Reds_r">Reds reversed</option>
+            <option value="Oranges_r">Oranges reversed</option>
+            <option value="Greens_r">Greens reversed</option>
+            <option value="Blues_r">Blues reversed</option>
+            <option value="Greys_r">Greys reversed</option>
+            <option value="Purples_r">Purples reversed</option>
+            <option value="Paired_r">Paired reversed</option>
+            <option value="Pastel1_r">Pastel1 reversed</option>
+            <option value="Pastel2_r">Pastel2 reversed</option>
+            <option value="spring_r">spring reversed</option>
+            <option value="summer_r">summer reversed</option>
+            <option value="autumn_r">autumn reversed</option>
+            <option value="winter_r">winter reversed</option>
+            <option value="hot_r">hot reversed</option>
+            <option value="coolwarm_r">coolwarm reversed</option>
+            <option value="cool_r">cool reversed</option>
+            <option value="seismic_r">seismic reversed</option>
+            <option value="terrain_r">terrain reversed</option>
+            <option value="ocean_r">ocean reversed</option>
+            <option value="rainbow_r">rainbow reversed</option>
+            <option value="bone_r">bone reversed</option>
+            <option value="flag_r">flag reversed</option>
+            <option value="prism_r">prism reversed</option>
+            <option value="cubehelix_r">cubehelix reversed</option>
+            <option value="binary_r">binary reversed</option>
+            <option value="pink_r">pink reversed</option>
+            <option value="gray_r">gray reversed</option>
+            <option value="copper_r">copper reversed</option>
+            <option value="BrBG_r">BrBG reversed</option>
+            <option value="BuGn_r">BuGn reversed</option>
+            <option value="BuPu_r">BuPu reversed</option>
+            <option value="GnBu_r">GnBu reversed</option>
+            <option value="OrRd_r">OrRd reversed</option>
+            <option value="PiYG_r">PiYG reversed</option>
+            <option value="PRGn_r">PRGn reversed</option>
+            <option value="PuOr_r">PuOr reversed</option>
+            <option value="PuRd_r">PuRd reversed</option>
+            <option value="PuBu_r">PuBu reversed</option>
+            <option value="RdBu_r">RdBu reversed</option>
+            <option value="RdGy_r">RdGy reversed</option>
+            <option value="RdPu_r">RdPu reversed</option>
+            <option value="YlGn_r">YlGn reversed</option>
+            <option value="PuBuGn_r">PuBuGn reversed</option>
+            <option value="RdYlBu_r">RdYlBu reversed</option>
+            <option value="RdYlGn_r">RdYlGn reversed</option>
+            <option value="YlGnBu_r">YlGnBu reversed</option>
+            <option value="YlOrBr_r">YlOrBr reversed</option>
+            <option value="YlOrRd_r">YlOrRd reversed</option>
+            <option value="gist_gray_r">gist_gray reversed</option>
+            <option value="gist_stern_r">gist_stern reversed</option>
+            <option value="gist_earth_r">gist_earth reversed</option>
+            <option value="gist_yarg_r">gist_yarg reversed</option>
+            <option value="gist_ncar_r">gist_ncar reversed</option>
+            <option value="gist_rainbow_r">gist_rainbow reversed</option>
+            <option value="gist_heat_r">gist_heat reversed</option>
+            <option value="gnuplot_r">gnuplot reversed</option>
+            <option value="gnuplot2_r">gnuplot2 reversed</option>
+            <option value="CMRmap_r">CMRmap reversed</option>
+            <option value="bwr_r">bwr reversed</option>
+            <option value="hsv_r">hsv reversed</option>
+            <option value="brg_r">brg reversed</option>
+            <option value="jet_r">jet reversed</option>
+            <option value="afmhot_r">afmhot reversed</option>
         </param>
-        
+
         <param name="zMin" type="float" value="" size="3" label="Minimum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
         <param name="zMax" type="float" value="" size="3" label="Maximum value for the heatmap intensities. Leave empty for automatic values" optional="true"/>
         <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
         <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
-        
+
         <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200" label="Description for the x-axis label" />
         <param name="yAxisLabel" type="text" value="genes" size="30" label="Description for the y-axis label for the top panel" />
-        
-        <param name="heatmapWidth" type="float" value="7.5" min="1" max="100" label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
 
+        <param name="heatmapWidth" type="float" value="7.5" min="1" max="100" label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
         <param name="heatmapHeight" type="float" value="25" min="3" max="100" label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
-        
+
         <param name="whatToShow" type="select" label="What to show" help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
           <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
           <option value="plot only">summary plot only</option>
@@ -305,16 +307,13 @@
           <option value="heatmap and colorbar">heatmap and colorbar</option>
           <option value="colorbar only">colorbar only</option>
         </param>
-        
+
         <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" help ="[only for scale-regions mode] Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
         <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
-        
+
         <param name="referencePointLabel" type="text" value="TSS" size="10" label="Reference point label" help ="[only for scale-regions mode] Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
-        
         <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
-        
         <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
-        
         <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
 
 
@@ -366,5 +365,4 @@
 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
   </help>
-
 </tool>
diff -r 09b65c12a75a -r 21d563d5f2b2 profiler.xml
--- a/profiler.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/profiler.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -3,12 +3,16 @@
     creates a profile plot for a score associated to genomic regions
   </description>
   <requirements>
-    <requirement type="package" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">deepTools</requirement>
+    <requirement type="package" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">deepTools</requirement>
   </requirements>
   <command>
   profiler
+
+  ##ToDo
+  --numberOfProcessors 4
+
   --matrixFile $matrixFile
-  
+
   #if $output.showOutputSettings == "yes"
       #set newoutFileName=str($outFileName)+"."+str($output.outFileFormat)
       --outFileName $newoutFilename
@@ -24,8 +28,8 @@
         --outFileSortedRegions '$output.outFileSortedRegions'
       #end if
   #else
-  #set newoutFileName=str($outFileName)+".png"
-  --outFileName $newoutFileName
+    #set newoutFileName=str($outFileName)+".png"
+    --outFileName $newoutFileName
   #end if
   
   #if $scaleRegions.showScaleRegionsOpt == "yes":
@@ -47,16 +51,16 @@
     #if str($advancedOpt.plotTitle.value) != "None":
       --plotTitle '$advancedOpt.plotTitle'
     #end if
-      
+
     $advancedOpt.onePlotPerGroup
-    
+
     #if $advancedOpt.yMin:
       --yMin $advancedOpt.yMin
     #end if
     #if $advancedOpt.yMax:
       --yMax $advancedOpt.yMax
     #end if
-      
+
     --xAxisLabel '$advancedOpt.xAxisLabel'
     #if str($advancedOpt.yAxisLabel.value) != "None":
       --yAxisLabel '$advancedOpt.yAxisLabel'
@@ -64,7 +68,6 @@
   #end if
   ; mv $newoutFileName $outFileName
   </command>
-
   <inputs>
     <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
     <conditional name="scaleRegions">
@@ -115,14 +118,12 @@
           <option value="sum">sum</option>
           <option value="std">std</option>
         </param>
-        
         <param name="plotHeight" type="integer" value="5" min="3" 
           label="Plot height" 
           help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
         <param name="plotWidth" type="integer" value="8" min="1" 
           label="Plot width" 
           help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
-        
         <param name="plotType" type="select" label="Plot type"
           help="For the summary plot (profile) only. The &quot;lines&quot; option will plot the profile line based on the average type selected. The &quot;fill&quot; option fills the region between zero and the profile curve. The fill in color is semi transparent to distinguish different profiles. The &quot;std&quot; option colors the region between the profile and the standard deviation of the data. As in the case of fill, a semi-transparent color is used. The option &quot;overlapped_lines&quot; plots each region values, one on top of the other; this option only works if &quot;one plot per proup&quot; is set.">
           <option value="lines" selected="true">lines</option>
@@ -134,10 +135,8 @@
         <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
         <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
         <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
-
         <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
         <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
-
         <param name="xAxisLabel" type="text" value="gene distance (bp)" size="50" label="Description for the x-axis label" />
         <param name="yAxisLabel" type="text" value="" size="50" label="Description for the y-axis label for the top panel" />
       </when>
@@ -185,5 +184,4 @@
 .. _Fidel Ramirez: ramirez@ie-freiburg.mpg.de
 
   </help>
-  
 </tool>
diff -r 09b65c12a75a -r 21d563d5f2b2 tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Aug 03 13:42:12 2013 -0400
+++ b/tool_dependencies.xml	Mon Aug 05 10:09:51 2013 -0400
@@ -1,53 +1,63 @@
-<?xml version="1.0"?>
+    <?xml version="1.0"?>
+<!--
+
+    <requirement type="package">deepTools</requirement>
+    <requirement type="python-module">deepTools</requirement> 
+    <requirement type="python-module">matplotlib</requirement> -> toolshed
+    <requirement type="python-module">argsparse</requirement> -> is in python 2.7 or?
+    <requirement type="python-module">itertools</requirement> -> is in standard python?
+    <requirement type="python-module">pysam</requirement> -> is also shipped with galaxy
+    <requirement type="python-module">numpy</requirement> -> toolshed
+    <requirement type="python-module">pylab</requirement> -> scipy toolshed
+    <requirement type="python-module">bx.intervals.io</requirement> -> bx-python is shipped with galaxy afaik
+-->
+
 <tool_dependency>
     <package name="samtools" version="0.1.18">
-        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_samtools_0_1_18" owner="devteam" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="40db34c904df" name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_numpy_1_7" owner="bgruening" prior_installation_required="True" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="dd81b71dff1b" name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_matplotlib_1_2" owner="bgruening" prior_installation_required="True" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="cd2e7872a8eb" name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository name="package_scipy_0_12" owner="bgruening" prior_installation_required="True" />
     </package>
 
-
     <package name="ucsc_tools" version="0.1">
         <install version="1.0">
             <actions>
                 <action type="download_binary">
-                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
-                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
-                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
+                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig</url_template>
+                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
+                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bedGraphToBigWig</url_template>
+                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bedGraphToBigWig</url_template>
                 </action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bedGraphToBigWig</file>
                 </action>
                 <action type="download_binary">
-                    <url_template architecture="x86_64" os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
-                    <url_template architecture="i686" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template architecture="i386" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
-                    <url_template architecture="x86_64" os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
+                    <url_template os="linux" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo</url_template>
+                    <url_template os="darwin" architecture="i686">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
+                    <url_template os="darwin" architecture="i386">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/bigWigInfo</url_template>
+                    <url_template os="darwin" architecture="x86_64">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/bigWigInfo</url_template>
                 </action>
                 <action type="chmod">
                     <file mode="755">$INSTALL_DIR/bigWigInfo</file>
                 </action>
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                 </action>
              </actions>
          </install>
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-
-    <package name="deepTools" version="1.5.1_98e5d8a61431ea8605c0643d991a1a5d8999b4dc">
+    <package name="deepTools" version="1.5.1_59e067cce039cb93add04823c9f51cab202f8c2b">
         <install version="1.0">
             <actions>
-
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
                 <action type="shell_command">git reset --hard 98e5d8a61431ea8605c0643d991a1a5d8999b4dc</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
@@ -57,8 +67,10 @@
                 </action>
 
                 <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PYTHONPATH" action="append_to" >$INSTALL_DIR/lib/python</environment_variable>
+                    <!-- disable the config file of deepTools -->
+                    <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable>
                 </action>
              </actions>
          </install>