# HG changeset patch
# User bgruening
# Date 1387186579 18000
# Node ID b4c5dd45778aaf4476c06a579dac1d196ad4a023
# Parent  aea72b24dea0f79aa0b234a588a03d73998bc632
Uploaded

diff -r aea72b24dea0 -r b4c5dd45778a bamFingerprint.xml
--- a/bamFingerprint.xml	Sat Dec 14 08:58:41 2013 -0500
+++ b/bamFingerprint.xml	Mon Dec 16 04:36:19 2013 -0500
@@ -26,12 +26,16 @@
       #set newoutFileName=str($outFileName)+".png"
       --plotFile $newoutFileName
 
-      #if $outputOpt.showOutputOpt == "yes"
-          #if $outputOpt.saveRawCounts:
+      #if $output.showOutputSettings == "yes"
+          --plotFileFormat $output.outFileFormat
+          #if $output.saveRawCounts:
             --outRawCounts '$outFileRawCounts' 
           #end if
+      #else
+        --plotFileFormat 'png'
       #end if
 
+
       #if $advancedOpt.showAdvancedOpt == "yes":
         
         #if str($advancedOpt.region.value) != '':
@@ -95,22 +99,28 @@
             </when>
         </conditional>
 
-        <conditional name="outputOpt">
-            <param name="showOutputOpt" type="select" label="Show additional output options" >
+        <conditional name="output">
+            <param name="showOutputSettings" type="select" label="Show advanced output settings">
                 <option value="no" selected="true">no</option>
                 <option value="yes">yes</option>
             </param>
             <when value="no" />
             <when value="yes">
+                <expand macro="input_image_file_format" />
                 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
             </when>
         </conditional>
 
     </inputs>
     <outputs>
-        <data format="png" name="outFileName" />
+        <expand macro="output_image_file_format" />
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
-            <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter>
+            <filter>
+            ((
+                outputOpt['showOutputOpt'] == 'yes' and 
+                outputOpt['saveRawCounts'] is True
+            ))
+            </filter>
         </data>
     </outputs>
     <help>
diff -r aea72b24dea0 -r b4c5dd45778a computeGCBias.xml
--- a/computeGCBias.xml	Sat Dec 14 08:58:41 2013 -0500
+++ b/computeGCBias.xml	Mon Dec 16 04:36:19 2013 -0500
@@ -10,7 +10,6 @@
         ln -s $bamInput.metadata.bam_index local_bamInput.bam.bai;
 
         computeGCBias
-
             @THREADS@
 
             --bamfile 'local_bamInput.bam'
@@ -42,79 +41,73 @@
                 #end if
             #end if
 
-            #if $saveBiasPlot:
-                --biasPlot $biasPlot
+            #if str($image_format) != 'none':
+                --biasPlot $outImageName
+                --plotFileFormat $image_format
             #end if
-
-        ##  #if $output.showOutputSettings == "yes"
-        ##      #if $output.saveBiasPlot:
-        ##        --biasPlot biasPlot.png ;
-        ##        mv biasPlot.png $biasPlot
-        ##      #end if
-        ##  #end if
-
     </command>
     <inputs>
-
         <param name="bamInput" format="bam" type="data" label="BAM file"
             help="The BAM file must be sorted."/>
 
         <expand macro="reference_genome_source" />
         <expand macro="effectiveGenomeSize" />
 
-      <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 from the BAM file."/>
+        <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 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;" />
+
+                <param name="sampleSize" type="integer" value="50000000" min="1"
+                    label="Number of sampling points to be considered" />
 
-    <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 name="regionSize" type="integer" value="300" min="1"
+                    label="Region size"
+                    help ="To plot the reads per GC over a region, the size of the region is required (see below for more details of the mthod). By default, the bin size is set to 300 bp, which is close to the standard fragment size many sequencing applications. However, if the depth of sequencing is low, a larger bin size will be required, otherwise many bins will not overlap with any read."/>
+
+                <param name="filterOut" type="data" format="bed" optional="true"
+                    label="BED file containing genomic regions to be excluded from the estimation of the correction"
+                    help="Such regions  usually contain repetitive regions and peaks that if included will bias the correction. It is recommended to filter out known repetitive regions if multi-reads (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, it is recommended to first use a peak caller to identify and filter out the identified peaks." />
+                <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>
+        <param name="image_format" type="select" label="GC bias plot" help="If given, a diagnostic image summarizing the GC bias found on the sample will be created.">
+            <option value="none" selected="true">No image</option>
+            <option value="png">Image in png format</option>
+            <option value="pdf">Image in pdf format</option>
+            <option value="svg">Image in svg format</option>
+            <option value="eps">Image in eps format</option>
+            <option value="emf">Image in emf format</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;" />
-             
-           <param name="sampleSize" type="integer" value="50000000" min="1"
-             label="Number of sampling points to be considered" />
-           
-           <param name="regionSize" type="integer" value="300" min="1"
-             label="Region size"
-             help ="To plot the reads per GC over a region, the size of the region is required (see below for more details of the mthod). By default, the bin size is set to 300 bp, which is close to the standard fragment size many sequencing applications. However, if the depth of sequencing is low, a larger bin size will be required, otherwise many bins will not overlap with any read."/>
-           
-           <param name="filterOut" type="data" format="bed" optional="true"
-             label="BED file containing genomic regions to be excluded from the estimation of the correction"
-             help="Such regions  usually contain repetitive regions and peaks that if included will bias the correction. It is recommended to filter out known repetitive regions if multi-reads (reads that map to more than one genomic position) were excluded. In the case of ChIP-seq data, it is recommended to first use a peak caller to identify and filter out the identified peaks." />
-           <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>
-
-    <param name="saveBiasPlot" type="boolean" truevalue="--biasPlot" falsevalue="" checked="True" label="Save a diagnostic image summarizing the GC bias found on the sample"/>
-    <!--
-    <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>
-      </param>
-      <when value="no" />
-      <when value="yes">
-        <param name="saveBiasPlot" type="boolean" label="Save a diagnostic image summarizing the GC bias found on the sample"/>
-      </when>
-    </conditional>
-    -->
-  </inputs>
-  <outputs>
-    <data format="tabular" name="outFileName" />
-    <data format="png" name="biasPlot" label="${tool.name} on ${on_string}: bias plot">
-      <filter>saveBiasPlot is True</filter>      
-      <!--<filter>(output['showOutputSettings'] == 'yes' and output['saveBiasPlot'] == True)</filter>-->
-    </data>
-  </outputs>
-  <help>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="outFileName" />
+        <data format="png" name="outImageName" label="${tool.name} GC-bias Plot">
+            <filter>
+            ((
+                image_format != 'none'
+            ))
+            </filter>
+            <change_format>
+                <when input="image_format" value="pdf" format="pdf" />
+                <when input="image_format" value="svg" format="svg" />
+                <when input="image_format" value="eps" format="eps" />
+                <when input="image_format" value="emf" format="emf" />
+            </change_format>
+        </data>
+    </outputs>
+    <help>
 
 **What it does**
 
diff -r aea72b24dea0 -r b4c5dd45778a computeMatrix.xml
--- a/computeMatrix.xml	Sat Dec 14 08:58:41 2013 -0500
+++ b/computeMatrix.xml	Mon Dec 16 04:36:19 2013 -0500
@@ -120,15 +120,15 @@
             <option	 value="TES">end of region (e.g. TES)</option>
             <option value="center">center of region</option>
         </param>
-        
         <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS."/>
         <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
-        
         <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
       </when>
     </conditional>
 
-    <expand macro="graphic_output_settings" />
+    <expand macro="input_graphic_output_settings">
+        <expand macro="input_save_matrix_values" />
+    </expand>
 
     <conditional name="advancedOpt" >
       <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -175,6 +175,7 @@
   <outputs>
     <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
     <expand macro="output_graphic_outputs" />
+    <expand macro="output_save_matrix_values" />
   </outputs>
     <!--
     computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 
diff -r aea72b24dea0 -r b4c5dd45778a correctGCBias.xml
--- a/correctGCBias.xml	Sat Dec 14 08:58:41 2013 -0500
+++ b/correctGCBias.xml	Mon Dec 16 04:36:19 2013 -0500
@@ -5,91 +5,84 @@
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
-  <command>
-    #import tempfile
-    #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+    <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))
+        #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
+        correctGCBias
 
-    @THREADS@
+        @THREADS@
 
-  --bamfile '$temp_bam_path'
-  --GCbiasFrequenciesFile $GCbiasFrequenciesFile
+        --bamfile '$temp_bam_path'
+        --GCbiasFrequenciesFile $GCbiasFrequenciesFile
 
-    @reference_genome_source@
+        @reference_genome_source@
 
 
-  #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
-    --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
-  #else:
-    --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
-  #end if
-
+        #if $effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
+            --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize
+        #else:
+            --effectiveGenomeSize $effectiveGenomeSize.effectiveGenomeSize_opt
+        #end if
 
-  #if $advancedOpt.showAdvancedOpt == "yes":
-    #if str($advancedOpt.region.value) != '':
-      --region '$advancedOpt.region'
-    #end if
-    
-    --binSize '$advancedOpt.binSize'  
-  #end if
-  
-  #set newoutFileName="corrected."+str($outFileFormat)
-  
-  --correctedFile $newoutFileName; mv $newoutFileName $outFileName
+        #if $advancedOpt.showAdvancedOpt == "yes":
+            #if str($advancedOpt.region.value) != '':
+                --region '$advancedOpt.region'
+            #end if
+            --binSize '$advancedOpt.binSize'  
+        #end if
 
-  </command>
-
-  <inputs>
+        #set newoutFileName="corrected."+str($outFileFormat)
+        --correctedFile $newoutFileName;
 
-  <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
-
-  <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
-
+        mv $newoutFileName $outFileName
+    </command>
+    <inputs>
+        <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
+        <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
         <expand macro="reference_genome_source" />
         <expand macro="effectiveGenomeSize" />
 
-  <param name="outFileFormat" type="select" label="File format of the output">
-    <option value="bam">bam</option>
-    <option value="bw">bigwig</option>
-    <option value="bg">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="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="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>
-  </inputs>
-  
-  <outputs>
-    <data format="bam" name="outFileName">
-    <change_format>
-        <when input="outFileFormat" value="bw" format="bigwig" />
-        <when input="outFileFormat" value="bam" format="bam" />
-        <when input="outFileFormat" value="bg" format="bedgraph" />
-    </change_format>
-    </data>
-  </outputs>
-  <help>
+        <param name="outFileFormat" type="select" label="File format of the output">
+            <option value="bam">bam</option>
+            <option value="bw">bigwig</option>
+            <option value="bg">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="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="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>
+    </inputs>
+    <outputs>
+        <data format="bam" name="outFileName">
+            <change_format>
+                <when input="outFileFormat" value="bw" format="bigwig" />
+                <when input="outFileFormat" value="bam" format="bam" />
+                <when input="outFileFormat" value="bg" format="bedgraph" />
+            </change_format>
+        </data>
+    </outputs>
+    <help>
 
 **What it does**
 
diff -r aea72b24dea0 -r b4c5dd45778a deepTools_macros.xml
--- a/deepTools_macros.xml	Sat Dec 14 08:58:41 2013 -0500
+++ b/deepTools_macros.xml	Mon Dec 16 04:36:19 2013 -0500
@@ -1,5 +1,5 @@
 <macros>
-    <macro name="bamCorrelate_mode_actions">
+    <xml name="bamCorrelate_mode_actions">
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                 <option value="no" selected="true">no</option>
@@ -36,14 +36,14 @@
                 <expand macro="colormap" />
             </when>
         </conditional>
-    </macro>
+    </xml>
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <macro name="requirements">
+    <xml name="requirements">
         <requirements>
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.4_6765c227d9628f8e6ba690e6fde7f1d86c497b49">deepTools</requirement>
+            <requirement type="package" version="1.5.4_74aac0843a956ca352e3e85087f20c8f158e2f7d">deepTools</requirement>
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.7">pysam</requirement>
@@ -53,18 +53,17 @@
             <requirement type="package" version="12-2013">bx-python</requirement>
             <yield />
         </requirements>
-    </macro>
-    <macro name="stdio">
+    </xml>
+    <xml name="stdio">
         <stdio>
             <exit_code range="1:" />
             <exit_code range=":-1" />
-            <exit_code range="0" level="warning" description="Warning" />
             <regex match="Error:" />
             <regex match="Exception:" />
             <regex match="EXception:" />
             <regex match="Traceback" />
         </stdio>
-    </macro>
+    </xml>
     <token name="@REFERENCES@">
 
 For more informations, please visit our `project site`_.
@@ -80,7 +79,7 @@
 
     </token>
 
-    <macro name="multiple_input_bams">
+    <xml name="multiple_input_bams">
         <repeat name="input_files" title="BAM files" min="2">
             <param name="bamfile" type="data" format="bam" 
                 label="Bam file" 
@@ -89,7 +88,7 @@
                 label="Label"
                 help="Label to use in the output. If not given the dataset name will be used instead."/>
           </repeat>
-    </macro>
+    </xml>
 
     <token name="@multiple_input_bams@">
         #for $i in $input_files:
@@ -109,7 +108,7 @@
         #end for
     </token>
 
-    <macro name="reference_genome_source">
+    <xml name="reference_genome_source">
         <conditional name="source">
             <param name="ref_source" type="select" label="Reference genome">
                 <option value="cached">locally cached</option>
@@ -127,7 +126,7 @@
                 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
             </when>
         </conditional>
-    </macro>
+    </xml>
 
     <token name="@reference_genome_source@">
     #if $source.ref_source=="history":
@@ -137,7 +136,7 @@
     #end if
     </token>
 
-    <macro name="effectiveGenomeSize">
+    <xml name="effectiveGenomeSize">
         <conditional name="effectiveGenomeSize">
             <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
                 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. 
@@ -153,9 +152,9 @@
                 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
             </when>
         </conditional>
-    </macro>
+    </xml>
 
-    <macro name="image_file_format">
+    <xml name="image_file_format">
         <param name="outFileFormat" type="select" label="Image file format">
             <option value="png" selected="true">png</option>
             <option value="pdf">pdf</option>
@@ -163,9 +162,13 @@
             <option value="eps">eps</option>
             <option value="emf">emf</option>
         </param>
-    </macro>
+    </xml>
 
-    <macro name="graphic_output_settings">
+    <xml name="input_save_matrix_values">
+        <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
+    </xml>
+
+    <xml name="input_graphic_output_settings">
         <conditional name="output" >
             <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                 <option value="no" selected="true">no</option>
@@ -174,14 +177,13 @@
             <when value="no" />
             <when value="yes">
                 <yield />
-                <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
-                <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
+                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
                 <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>
-    </macro>
+    </xml>
 
-    <macro name="input_image_file_format">
+    <xml name="input_image_file_format">
         <param name="outFileFormat" type="select" label="Image file format">
             <option value="png" selected="true">png</option>
             <option value="pdf">pdf</option>
@@ -189,9 +191,9 @@
             <option value="eps">eps</option>
             <option value="emf">emf</option>
         </param>
-    </macro>
+    </xml>
 
-    <macro name="output_image_file_format">
+    <xml name="output_image_file_format">
         <data format="png" name="outFileName" label="${tool.name} image">
             <change_format>
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
@@ -200,10 +202,20 @@
                 <when input="output.outFileFormat" value="emf" format="emf" />
             </change_format>
         </data>
-    </macro>
+    </xml>
 
-    <macro name="output_graphic_outputs">
-        <yield />
+    <xml name="output_save_matrix_values">
+        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and 
+                output['saveMatrix'] is True
+            ))
+            </filter>
+        </data>
+    </xml>
+
+    <xml name="output_graphic_outputs">
         <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
             <filter>
             ((
@@ -212,14 +224,6 @@
             ))
             </filter>
         </data>
-        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
-            <filter>
-            ((
-                output['showOutputSettings'] == 'yes' and 
-                output['saveMatrix'] is True
-            ))
-            </filter>
-        </data>
         <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
             <filter>
             ((
@@ -228,9 +232,9 @@
             ))
             </filter>
         </data>
-    </macro>
+    </xml>
 
-    <macro name="colormap">
+    <xml name="colormap">
         <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
             <option value="RdYlBu" selected="true">RdYlBu</option>
             <option value="Accent">Accent</option>
@@ -372,6 +376,6 @@
             <option value="afmhot_r">afmhot reversed</option>
         </param>
 
-    </macro>
+    </xml>
 
 </macros>
diff -r aea72b24dea0 -r b4c5dd45778a heatmapper.xml
--- a/heatmapper.xml	Sat Dec 14 08:58:41 2013 -0500
+++ b/heatmapper.xml	Mon Dec 16 04:36:19 2013 -0500
@@ -91,8 +91,9 @@
     <inputs>
         <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
 
-        <expand macro="graphic_output_settings">
+        <expand macro="input_graphic_output_settings">
             <expand macro="input_image_file_format" />
+            <expand macro="input_save_matrix_values" />
         </expand>
 
         <conditional name="advancedOpt" >
@@ -176,9 +177,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <expand macro="output_graphic_outputs">
-            <expand macro="output_image_file_format" />
-        </expand>
+        <expand macro="output_image_file_format" />
+        <expand macro="output_graphic_outputs" />
+        <expand macro="output_save_matrix_values" />
     </outputs>
     <tests>
         <test>
diff -r aea72b24dea0 -r b4c5dd45778a profiler.xml
--- a/profiler.xml	Sat Dec 14 08:58:41 2013 -0500
+++ b/profiler.xml	Mon Dec 16 04:36:19 2013 -0500
@@ -20,10 +20,6 @@
                 --outFileNameData '$outFileNameData' 
             #end if
 
-            #if $output.saveMatrix:
-                --outFileNameMatrix '$outFileNameMatrix'
-            #end if
-
             #if $output.saveSortedRegions:
                 --outFileSortedRegions '$outFileSortedRegions'
             #end if
@@ -79,7 +75,7 @@
             </when>
         </conditional>
 
-        <expand macro="graphic_output_settings">
+        <expand macro="input_graphic_output_settings">
             <expand macro="input_image_file_format" />
         </expand>
 
@@ -122,9 +118,8 @@
         </conditional>
     </inputs>
     <outputs>
-        <expand macro="output_graphic_outputs">
-            <expand macro="output_image_file_format" />
-        </expand>
+        <expand macro="output_image_file_format" />
+        <expand macro="output_graphic_outputs" />
     </outputs>
     <help>
 
diff -r aea72b24dea0 -r b4c5dd45778a tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Dec 14 08:58:41 2013 -0500
+++ b/tool_dependencies.xml	Mon Dec 16 04:36:19 2013 -0500
@@ -57,7 +57,7 @@
          <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="1.5.4_6765c227d9628f8e6ba690e6fde7f1d86c497b49">
+    <package name="deepTools" version="1.5.4_74aac0843a956ca352e3e85087f20c8f158e2f7d">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
@@ -69,8 +69,17 @@
                     <repository changeset_revision="f938170835cc" name="package_bx_python_12_2013" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                         <package name="bx-python" version="12-2013" />
                     </repository>
+                    <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                    </repository>
+                    <repository changeset_revision="dceff6072512" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="matplotlib" version="1.2.1" />
+                    </repository>
+                    <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="scipy" version="0.12.0" />
+                    </repository>
                 </action>
-                <action type="shell_command">git reset --hard 6765c227d9628f8e6ba690e6fde7f1d86c497b49</action>
+                <action type="shell_command">git reset --hard 74aac0843a956ca352e3e85087f20c8f158e2f7d</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;