# HG changeset patch
# User bgruening
# Date 1386974310 18000
# Node ID e43b4015b4ccb6e633aa12c4e7e28212813818b3
# Parent  b8ba675a589544ef630564c2d374e54a54add721
Uploaded

diff -r b8ba675a5895 -r e43b4015b4cc bamCompare.xml
--- a/bamCompare.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/bamCompare.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCompare" name="bamCompare" version="1.0">
+<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.2">
     <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
diff -r b8ba675a5895 -r e43b4015b4cc bamCorrelate.xml
--- a/bamCorrelate.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/bamCorrelate.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.1">
+<tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.2">
     <description>correlates pairs of BAM files</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -6,9 +6,6 @@
         <import>deepTools_macros.xml</import>
     </macros>
     <command>
-        #import tempfile
-        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
-
         #set files=[]
         #set labels=[]
 
@@ -22,16 +19,17 @@
 
         --bamfiles #echo " ".join($files)
         --labels #echo " ".join($labels)
-
         --fragmentLength $fragmentLength
         --corMethod $corMethod
 
-        #set newoutFileName=str($outFileName)+".png"
-        --plotFile $newoutFileName
+        --plotFile $outFileName
 
         #if $outputOpt.showOutputOpt == "yes"
             --outRawCounts '$outFileRawCounts' 
             --outFileCorMatrix '$outFileCorMatrix'
+            --plotFileFormat $output.outFileFormat
+        #else:
+            --plotFileFormat 'png'
         #end if
 
         #if $mode.modeOpt == "bins":
@@ -65,9 +63,6 @@
             --colorMap '$mode.advancedOpt.colorMap'
 
         #end if
-
-        ; mv $newoutFileName $outFileName
-        ; rm $temp_dir -rf
     </command>
 
     <inputs>
@@ -112,6 +107,13 @@
             </param>
             <when value="no" />
             <when value="yes">
+                <param name="outFileFormat" type="select" label="Image file format">
+                    <option value="png" selected="true">png</option>
+                    <option value="pdf">pdf</option>
+                    <option value="svg">svg</option>
+                    <option value="eps">eps</option>
+                    <option value="emf">emf</option>
+                </param>
                 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
                 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
             </when>
@@ -119,7 +121,14 @@
 
     </inputs>
     <outputs>
-        <data format="png" name="outFileName" />
+        <data format="png" name="outFileName">
+            <change_format>
+                <when input="output.outFileFormat" value="pdf" format="pdf" />
+                <when input="output.outFileFormat" value="svg" format="svg" />
+                <when input="output.outFileFormat" value="eps" format="eps" />
+                <when input="output.outFileFormat" value="emf" format="emf" />
+            </change_format>
+        </data>
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
             <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter>
         </data>
diff -r b8ba675a5895 -r e43b4015b4cc bamCoverage.xml
--- a/bamCoverage.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/bamCoverage.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0">
+<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.2">
     <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
diff -r b8ba675a5895 -r e43b4015b4cc bamFingerprint.xml
--- a/bamFingerprint.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/bamFingerprint.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0">
+<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.2">
     <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
diff -r b8ba675a5895 -r e43b4015b4cc bigwigCompare.xml
--- a/bigwigCompare.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/bigwigCompare.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0">
+<tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0.2">
     <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
     <expand macro="requirements"/>
     <expand macro="stdio" />
diff -r b8ba675a5895 -r e43b4015b4cc computeGCBias.xml
--- a/computeGCBias.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/computeGCBias.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.1">
+<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.2">
     <description>to see whether your samples should be normalized for GC bias</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
diff -r b8ba675a5895 -r e43b4015b4cc computeMatrix.xml
--- a/computeMatrix.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/computeMatrix.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0">
+<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.2">
     <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>
     <expand macro="requirements" />
     <expand macro="stdio" />
diff -r b8ba675a5895 -r e43b4015b4cc correctGCBias.xml
--- a/correctGCBias.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/correctGCBias.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.1">
+<tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.2">
     <description>uses the output from computeGCBias to generate corrected BAM files</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
diff -r b8ba675a5895 -r e43b4015b4cc deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/deepTools_macros.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -43,7 +43,7 @@
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">deepTools</requirement>
+            <requirement type="package" version="1.5.4_6765c227d9628f8e6ba690e6fde7f1d86c497b49">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>
@@ -172,7 +172,13 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <yield />
+                <param name="outFileFormat" type="select" label="Image file format">
+                    <option value="png" selected="true">png</option>
+                    <option value="pdf">pdf</option>
+                    <option value="svg">svg</option>
+                    <option value="eps">eps</option>
+                    <option value="emf">emf</option>
+                </param>
                 <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="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."/>
@@ -181,6 +187,14 @@
     </macro>
 
     <macro name="output_graphic_outputs">
+        <data format="png" name="outFileName" label="${tool.name} image">
+            <change_format>
+                <when input="output.outFileFormat" value="pdf" format="pdf" />
+                <when input="output.outFileFormat" value="svg" format="svg" />
+                <when input="output.outFileFormat" value="eps" format="eps" />
+                <when input="output.outFileFormat" value="emf" format="emf" />
+            </change_format>
+        </data>
         <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
             <filter>
             ((
diff -r b8ba675a5895 -r e43b4015b4cc heatmapper.xml
--- a/heatmapper.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/heatmapper.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,184 +1,175 @@
-<tool id="deeptools_heatmapper" name="heatmapper" version="1.0">
+<tool id="deeptools_heatmapper" name="heatmapper" version="1.0.2">
     <description>creates a heatmap for a score associated to genomic regions</description>
     <expand macro="requirements"/>
     <expand macro="stdio" />
     <macros>
         <import>deepTools_macros.xml</import>
     </macros>
-  <command>
-  heatmapper
+    <command>
+        heatmapper
+
+        --matrixFile $matrixFile
+        --outFileName $outFileName
 
-  --matrixFile $matrixFile
-  #if $output.showOutputSettings == "yes"
-      #set newoutFileName=str($outFileName)+"."+str($output.outFileFormat)
-      --outFileName $newoutFileName
-      #if $outFileNameData:
-        --outFileNameData '$outFileNameData'
-      #end if
-
-      #if $outFileNameMatrix:
-      --outFileNameMatrix '$outFileNameMatrix'
-      #end if
+        #if $output.showOutputSettings == "yes"
+            --plotFileFormat $output.outFileFormat
+            #if $outFileNameData:
+                --outFileNameData '$outFileNameData'
+            #end if
 
-      #if $outFileSortedRegions:
-        --outFileSortedRegions '$outFileSortedRegions'
-      #end if
-  #else
-    #set newoutFileName=str($outFileName)+".png"
-    --outFileName $newoutFileName
-  #end if
-  
-  #if $advancedOpt.showAdvancedOpt == "yes"
-      #if $advancedOpt.sortRegions:
-        --sortRegions '$advancedOpt.sortRegions'
-      #end if
-      
-      #if $advancedOpt.sortUsing:
-        --sortUsing '$advancedOpt.sortUsing'
-      #end if
-      
-      #if $advancedOpt.averageTypeSummaryPlot:
-        --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
-      #end if
-      
-      #if str($advancedOpt.missingDataColor.value) != "None":
-        --missingDataColor '$advancedOpt.missingDataColor'
-      #end if
+            #if $outFileNameMatrix:
+                --outFileNameMatrix '$outFileNameMatrix'
+            #end if
+
+            #if $outFileSortedRegions:
+                --outFileSortedRegions '$outFileSortedRegions'
+            #end if
+        #else
+            --plotFileFormat 'png'
+        #end if
+
+        #if $advancedOpt.showAdvancedOpt == "yes"
+            #if $advancedOpt.sortRegions:
+                --sortRegions '$advancedOpt.sortRegions'
+            #end if
       
-      --colorMap '$advancedOpt.colorMap'
-      
-      #if $advancedOpt.zMin:
-        --zMin $advancedOpt.zMin
-      #end if
-      #if $advancedOpt.zMax:
-        --zMax $advancedOpt.zMax
-      #end if
-      
-      #if $advancedOpt.yMin:
-        --yMin $advancedOpt.yMin
-      #end if
-      #if $advancedOpt.yMax:
-        --yMax $advancedOpt.yMax
-      #end if
+            #if $advancedOpt.sortUsing:
+                --sortUsing '$advancedOpt.sortUsing'
+            #end if
+
+            #if $advancedOpt.averageTypeSummaryPlot:
+                --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
+            #end if
 
-      --xAxisLabel '$advancedOpt.xAxisLabel'
-      --yAxisLabel '$advancedOpt.yAxisLabel'
+            #if str($advancedOpt.missingDataColor.value) != "None":
+                --missingDataColor '$advancedOpt.missingDataColor'
+            #end if
+
+            --colorMap '$advancedOpt.colorMap'
+
+            #if $advancedOpt.zMin:
+                --zMin $advancedOpt.zMin
+            #end if
+            #if $advancedOpt.zMax:
+                --zMax $advancedOpt.zMax
+            #end if
 
-      --heatmapWidth $advancedOpt.heatmapWidth
-      --heatmapHeight $advancedOpt.heatmapHeight
-
-      --whatToShow '$advancedOpt.whatToShow'
+            #if $advancedOpt.yMin:
+                --yMin $advancedOpt.yMin
+            #end if
+            #if $advancedOpt.yMax:
+                --yMax $advancedOpt.yMax
+            #end if
 
-      --startLabel '$advancedOpt.startLabel' 
-      --endLabel '$advancedOpt.endLabel'
-      --refPointLabel '$advancedOpt.referencePointLabel'
-      --regionsLabel '$advancedOpt.regionsLabel'
+            --xAxisLabel '$advancedOpt.xAxisLabel'
+            --yAxisLabel '$advancedOpt.yAxisLabel'
+
+            --heatmapWidth $advancedOpt.heatmapWidth
+            --heatmapHeight $advancedOpt.heatmapHeight
+
+            --whatToShow '$advancedOpt.whatToShow'
 
-      #if str($advancedOpt.plotTitle.value) != "None":
-      --plotTitle '$advancedOpt.plotTitle'
-      #end if
+            --startLabel '$advancedOpt.startLabel' 
+            --endLabel '$advancedOpt.endLabel'
+            --refPointLabel '$advancedOpt.referencePointLabel'
+            --regionsLabel '$advancedOpt.regionsLabel'
 
-      $advancedOpt.onePlotPerGroup
-  #end if
+            #if str($advancedOpt.plotTitle.value) != "None":
+                --plotTitle '$advancedOpt.plotTitle'
+            #end if
 
-  ; mv $newoutFileName $outFileName
-  </command>
-  <inputs>
-    <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
+            $advancedOpt.onePlotPerGroup
+        #end if
+    </command>
+    <inputs>
+        <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
 
-    <expand macro="graphic_output_settings">
-        <expand macro="image_file_format" />
-    <expand>
+        <expand macro="graphic_output_settings" />
 
-    <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="sortRegions" type="select" label="Sort regions"
-           help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
-          <option value="no">no ordering</option>
-          <option value="descend" selected="true">descending order</option>
-          <option value="ascend">ascending order</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="sortRegions" type="select" label="Sort regions"
+                    help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
+                    <option value="no">no ordering</option>
+                    <option value="descend" selected="true">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>
-          <option value="min">min</option>
-          <option value="max">max</option>
-          <option value="sum">sum</option>
-          <option value="region_length">region length</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>
+                    <option value="min">min</option>
+                    <option value="max">max</option>
+                    <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>
-          <option value="min">min</option>
-          <option value="max">max</option>
-          <option value="sum">sum</option>
-          <option value="std">std</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>
+                    <option value="min">min</option>
+                    <option value="max">max</option>
+                    <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="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." />
 
-        <expand macro="colormap" />
+                <expand macro="colormap" />
 
-        <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="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="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="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="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>
-          <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
-          <option value="heatmap only">heatmap only</option>
-          <option value="heatmap and colorbar">heatmap and colorbar</option>
-          <option value="colorbar only">colorbar only</option>
-        </param>
+                <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="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="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>
+                    <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
+                    <option value="heatmap only">heatmap only</option>
+                    <option value="heatmap and colorbar">heatmap and colorbar</option>
+                    <option value="colorbar only">colorbar only</option>
+                </param>
 
-        <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."/>
-
-
-      </when>
-    </conditional>
+                <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)."/>
 
-  </inputs>
-  <outputs>
-    <data format="png" name="outFileName" label="${tool.name} image">
-        <change_format>
-            <when input="output.outFileFormat" value="pdf" format="pdf" />
-            <when input="output.outFileFormat" value="svg" format="svg" />
-            <when input="output.outFileFormat" value="eps" format="eps" />
-            <when input="output.outFileFormat" value="emf" format="emf" />
-        </change_format>
-    </data>
-
-    <expand macro="output_graphic_outputs" />
-
-  </outputs>
+                <param name="referencePointLabel" type="text" value="TSS" size="10" label="Reference point label" help ="[only for scale-regions mode] Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
+                <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
+                <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
+                <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="png" name="outFileName" label="${tool.name} image">
+            <change_format>
+                <when input="output.outFileFormat" value="pdf" format="pdf" />
+                <when input="output.outFileFormat" value="svg" format="svg" />
+                <when input="output.outFileFormat" value="eps" format="eps" />
+                <when input="output.outFileFormat" value="emf" format="emf" />
+            </change_format>
+        </data>
+        <expand macro="output_graphic_outputs" />
+    </outputs>
     <tests>
         <test>
             <param name="matrixFile" value="master.mat.gz" ftype="bgzip" />
             <output name="outFileName" file="master.png" ftype="png" compare="sim_size" delta="100" />
         </test>
     </tests>
-  <help>
+    <help>
 
 **What it does**
 
diff -r b8ba675a5895 -r e43b4015b4cc profiler.xml
--- a/profiler.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/profiler.xml	Fri Dec 13 17:38:30 2013 -0500
@@ -1,4 +1,4 @@
-<tool id="deeptools_profiler" name="profiler" version="1.0">
+<tool id="deeptools_profiler" name="profiler" version="1.0.2">
     <description>
         creates a profile plot for a score associated to genomic regions
     </description>
@@ -11,10 +11,10 @@
         profiler
 
         --matrixFile $matrixFile
+        --outFileName $outFileName
 
         #if $output.showOutputSettings == "yes"
-            #set newoutFileName = str($outFileName)+"."+str($output.outFileFormat)
-            --outFileName $newoutFileName
+            --plotFileFormat $output.outFileFormat
 
             #if $output.saveData:
                 --outFileNameData '$outFileNameData' 
@@ -28,8 +28,7 @@
                 --outFileSortedRegions '$outFileSortedRegions'
             #end if
         #else
-            #set newoutFileName = str($outFileName)+".png"
-            --outFileName $newoutFileName
+            --plotFileFormat 'png'
         #end if
 
         #if $scaleRegions.showScaleRegionsOpt == "yes":
@@ -65,7 +64,6 @@
                 --yAxisLabel '$advancedOpt.yAxisLabel'
             #end if
         #end if
-        ; mv $newoutFileName $outFileName
     </command>
     <inputs>
         <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
@@ -113,7 +111,6 @@
                     <option value="std">std</option>
                     <option value="overlapped_lines">overlapped lines</option>
                 </param>
-
                 <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
                 <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
                 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
@@ -125,14 +122,6 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="png" name="outFileName" label="${tool.name} image">
-            <change_format>
-                <when input="output.outFileFormat" value="pdf" format="pdf" />
-                <when input="output.outFileFormat" value="svg" format="svg" />
-                <when input="output.outFileFormat" value="eps" format="eps" />
-                <when input="output.outFileFormat" value="emf" format="emf" />
-            </change_format>
-        </data>
         <expand macro="output_graphic_outputs" />
     </outputs>
     <help>
diff -r b8ba675a5895 -r e43b4015b4cc tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Dec 12 18:13:18 2013 -0500
+++ b/tool_dependencies.xml	Fri Dec 13 17:38:30 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_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">
+    <package name="deepTools" version="1.5.4_6765c227d9628f8e6ba690e6fde7f1d86c497b49">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
@@ -70,7 +70,7 @@
                         <package name="bx-python" version="12-2013" />
                     </repository>
                 </action>
-                <action type="shell_command">git reset --hard fada41ab04f78c4c78d10c7a216e5c3160e8c36e</action>
+                <action type="shell_command">git reset --hard 6765c227d9628f8e6ba690e6fde7f1d86c497b49</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;