# HG changeset patch
# User galaxyp
# Date 1433008546 14400
# Node ID 1dbd76a58d8b6ba9f33d88c559ad04198ad8308a
# Parent  9bee2c86eeb1ecc56e9e2d7e78bacd9e44ba27ae
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty

diff -r 9bee2c86eeb1 -r 1dbd76a58d8b bamCompare.xml
--- a/bamCompare.xml	Mon May 25 05:16:10 2015 -0400
+++ b/bamCompare.xml	Sat May 30 13:55:46 2015 -0400
@@ -109,10 +109,15 @@
 
         <conditional name="comparison">
             <param name="type" type="select" 
-                label="How to compare the two files">
+                label="How to compare the two files"
+                help="The default is to output the log2ratio between the two samples.
+                The reciprocal ratio returns the negative of the inverse of the ratio if
+                the ratio is less than 0. The resulting values are interpreted as negative fold changes.">
                 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
                 <option value="ratio">Compute the ratio of the number of reads</option>
                 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
+                <option value="add">Compute the sum of number of reads</option>
+                <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
             </param>
             <when value="log2">
                 <expand macro="pseudocount" />
@@ -120,6 +125,10 @@
             <when value="ratio">
                 <expand macro="pseudocount" />
             </when>
+            <when value="add" />
+            <when value="reciprocal_ratio">
+                <expand macro="pseudocount" />
+            </when>
             <when value="subtract">
                 <conditional name="normalization">
                     <param name="type" type="select" label="Normalization method" >
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b bamFingerprint.xml
--- a/bamFingerprint.xml	Mon May 25 05:16:10 2015 -0400
+++ b/bamFingerprint.xml	Sat May 30 13:55:46 2015 -0400
@@ -112,7 +112,7 @@
             <param name="fragmentLength" value="200" />
             <param name="showAdvancedOpt" value="no" />
             <param name="showOutputSettings" value="no" />
-            <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" />
+            <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" compare="sim_size" />
         </test>
     </tests>
     <help>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b bamPEFragmentSize.xml
--- a/bamPEFragmentSize.xml	Mon May 25 05:16:10 2015 -0400
+++ b/bamPEFragmentSize.xml	Sat May 30 13:55:46 2015 -0400
@@ -35,7 +35,7 @@
             <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
             <param name="histogram" value="True" />
             <output name="outfile" file="bamPEFragmentSize_result1.txt" ftype="txt" />
-            <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" />
+            <output name="histogram_outfile" file="bamPEFragmentSize_histogram_result1.png" ftype="png" compare="sim_size" />
         </test>
     </tests>
     <help>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b bigwigCompare.xml
--- a/bigwigCompare.xml	Mon May 25 05:16:10 2015 -0400
+++ b/bigwigCompare.xml	Sat May 30 13:55:46 2015 -0400
@@ -46,12 +46,15 @@
 
         <conditional name="comparison">
             <param name="comparison_select" type="select" 
-                label="How to compare the two files" help="(--ratio)">
+                label="How to compare the two files"
+                help="The default is to output the log2ratio between the two samples.
+                The reciprocal ratio returns the negative of the inverse of the ratio if
+                the ratio is less than 0. The resulting values are interpreted as negative fold changes. (--ratio)">
                 <option value="log2" selected="true">compute log2 of the number of reads ratio</option>
                 <option value="ratio">compute the ratio of the number of reads</option>
                 <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option>
                 <option value="add">compute the sum over all reads</option>
-                <option value="reciprocal_ratio">compute the reciprocal ratio of the number of reads</option>
+                <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
             </param>
             <when value="log2">
                 <expand macro="pseudocount" />
@@ -61,7 +64,9 @@
             </when>
             <when value="subtract" />
             <when value="add" />
-            <when value="reciprocal_ratio" />
+            <when value="reciprocal_ratio">
+                <expand macro="pseudocount" />
+            </when>
         </conditional>
 
         <param name="outFileFormat" type="select" label="Coverage file format">
@@ -107,8 +112,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="bigwigFile1" value="1.bigwig" ftype="bigwig" />
-            <param name="bigwigFile2" value="1.bigwig" ftype="bigwig" />
+            <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
+            <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="no" />
             <param name="outFileFormat" value="bigwig" />
             <param name="binSize" value="5" />
@@ -116,8 +121,8 @@
             <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" />
         </test>
         <test>
-            <param name="bigwigFile1" value="1.bigwig" ftype="bigwig" />
-            <param name="bigwigFile2" value="1.bigwig" ftype="bigwig" />
+            <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
+            <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="no" />
             <param name="outFileFormat" value="bedgraph" />
             <param name="binSize" value="10" />
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b bigwigCorrelate.xml
--- a/bigwigCorrelate.xml	Mon May 25 05:16:10 2015 -0400
+++ b/bigwigCorrelate.xml	Sat May 30 13:55:46 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCorrelate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
+<tool id="deeptools_bigwigCorrelate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
     <description>correlates pairs of BigWig files</description>
     <macros>
         <token name="@BINARY@">bigwigCorrelate</token>
@@ -143,16 +143,17 @@
     <tests>
         <test>
             <repeat name="input_files">
-                <param name="bigwigfile" value="1.bigwig" ftype="bigwig" />
+                <param name="bigwigfile" value="test.bw" ftype="bigwig" />
                 <param name="label" value="first bigwig file" />
             </repeat>
             <repeat name="input_files">
-                <param name="bigwigfile" value="1.bigwig" ftype="bigwig" />
+                <param name="bigwigfile" value="test.bw" ftype="bigwig" />
                 <param name="label" value="second bigwig file" />
             </repeat>
             <param name="modeOpt" value="bins" />
             <param name="binSize" value="10" />
             <param name="showOutputSettings" value="no" />
+            <param name="corMethod" value="spearman" />
             <output name="outFileName" file="bigwigCorrelate_result1.png" ftype="png" compare="sim_size" />
         </test>
     </tests>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b computeGCBias.xml
--- a/computeGCBias.xml	Mon May 25 05:16:10 2015 -0400
+++ b/computeGCBias.xml	Sat May 30 13:55:46 2015 -0400
@@ -113,15 +113,19 @@
     </outputs>
     <tests>
         <test>
-            <param name="bamInput" value="phiX.bam" ftype="bam" />
+            <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
             <param name="image_format" value="png" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="regionSize" value="1" />
             <param name="fragmentLength" value="100" />
             <param name="ref_source" value="history" />
-            <param name="input1" value="phiX.2bit" />
+            <param name="input1" value="sequence.2bit" />
+            <param name="sampleSize" value="10" />
+            <param name="effectiveGenomeSize_opt" value="specific" />
+            <param name="effectiveGenomeSize" value="23011544" />
+            <param name="region" value="chr2L" />
+            <param name="image_format" value="none" />
             <output name="outFileName" file="computeGCBias_result1.tabular" ftype="tabular" />
-            <output name="outImageName" file="computeGCBias_result1.png" ftype="png" />
         </test>
     </tests>
     <help>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b computeMatrix.xml
--- a/computeMatrix.xml	Mon May 25 05:16:10 2015 -0400
+++ b/computeMatrix.xml	Sat May 30 13:55:46 2015 -0400
@@ -63,13 +63,13 @@
                 $advancedOpt.skipZeros
                 --binSize $advancedOpt.binSize
 
-                #if $advancedOpt.minThreshold:
+                #if $advancedOpt.minThreshold is not None and str($advancedOpt.minThreshold) != '':
                     --minThreshold $advancedOpt.minThreshold
                 #end if
-                #if $advancedOpt.maxThreshold:
+                #if $advancedOpt.maxThreshold is not None and str($advancedOpt.maxThreshold) != '':
                     --maxThreshold $advancedOpt.maxThreshold
                 #end if
-                #if $advancedOpt.scale:
+                #if $advancedOpt.scale is not None and str($advancedOpt.scale) != '':
                     --scale $advancedOpt.scale
                 #end if
 
@@ -223,7 +223,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="deeptools_matrix" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
+        <data format="deeptools_compute_matrix_archive" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
         <expand macro="output_graphic_outputs" />
         <expand macro="output_save_matrix_values" />
     </outputs>
@@ -242,7 +242,7 @@
             <param name="missingDataAsZero" value="True" />
             <param name="beforeRegionStartLength" value="10" />
             <param name="afterRegionStartLength" value="10" />
-            <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_matrix" compare="sim_size" />
+            <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
@@ -252,7 +252,7 @@
             <param name="binSize" value="10" />
             <param name="beforeRegionStartLength" value="10" />
             <param name="afterRegionStartLength" value="10" />
-            <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_matrix" compare="sim_size" />
+            <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_compute_matrix_archive" compare="sim_size" />
         </test>
     </tests>
   <help>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b correctGCBias.xml
--- a/correctGCBias.xml	Mon May 25 05:16:10 2015 -0400
+++ b/correctGCBias.xml	Sat May 30 13:55:46 2015 -0400
@@ -26,7 +26,9 @@
             #if str($region).strip() != '':
                 --region '$region'
             #end if
-            --correctedFile $outFileName
+            --correctedFile corrected.bam;
+
+        mv corrected.bam $outFileName;
 ]]>
     </command>
     <inputs>
@@ -43,12 +45,12 @@
     <tests>
         <test>
             <param name="GCbiasFrequenciesFile" value="computeGCBias_result1.tabular" ftype="tabular" />
-            <param name="bamInput" value="phiX.bam" ftype="bam" />
+            <param name="bamInput" value="paired_chr2L.bam" ftype="bam" />
             <param name="ref_source" value="history" />
-            <param name="input1" value="phiX.2bit" />
+            <param name="input1" value="sequence.2bit" />
             <param name="effectiveGenomeSize_opt" value="specific" />
-            <param name="effectiveGenomeSize" value="5386" />
-            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" compare="sim_size" />
+            <param name="effectiveGenomeSize" value="23011544" />
+            <output name="outFileName" file="correctGCBias_result1.bam" ftype="bam" />
         </test>
     </tests>
     <help>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b datatypes_conf.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/datatypes_conf.xml	Sat May 30 13:55:46 2015 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<datatypes>
+    <registration>
+        <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
+    </registration>
+</datatypes>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b deepTools_macros.xml
--- a/deepTools_macros.xml	Mon May 25 05:16:10 2015 -0400
+++ b/deepTools_macros.xml	Sat May 30 13:55:46 2015 -0400
@@ -79,7 +79,7 @@
                 label="Did you compute the matrix with more than one groups of regions?"
                 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
                 <option value="yes">Yes, I used multiple groups of regions</option>
-                <option value="no">No, I used only one region.</option>
+                <option value="no">No, I used only one group</option>
             </param>
             <when value="no">
                 <conditional name="clustering">
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b heatmapper.xml
--- a/heatmapper.xml	Mon May 25 05:16:10 2015 -0400
+++ b/heatmapper.xml	Sat May 30 13:55:46 2015 -0400
@@ -102,13 +102,14 @@
             <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.">
+                    help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region. (--sortRegions)">
                     <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." >
+                <param name="sortUsing" type="select" label="Method used for sorting"
+                    help="For each row the method is computed. (--sortUsing)">
                     <option value="mean" selected="true">mean</option>
                     <option value="median">median</option>
                     <option value="min">min</option>
@@ -117,7 +118,9 @@
                     <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">
+                <param name="averageTypeSummaryPlot" type="select"
+                    label="Type of statistic that should be plotted in the summary image above the heatmap"
+                    help="(--averageTypeSummaryPlot)">
                     <option value="mean" selected="true">mean</option>
                     <option value="median">median</option>
                     <option value="min">min</option>
@@ -127,22 +130,25 @@
                 </param>
 
                 <param name="missingDataColor" type="text" value="black" optional="true" label="Missing data color" 
-                    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." />
+                    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. (--missingDataColor)" />
 
                 <expand macro="colormap" />
 
                 <param name="zMin" type="float" value="" size="3"
-                    label="Minimum value for the heatmap intensities. Leave empty for automatic values"/>
+                    label="Minimum value for the heatmap intensities. Leave empty for automatic values" help="(--zMin)"/>
                 <param name="zMax" type="float" value="" size="3"
-                    label="Maximum value for the heatmap intensities. Leave empty for automatic values"/>
+                    label="Maximum value for the heatmap intensities. Leave empty for automatic values" help="(--zMax)"/>
                 <param name="yMin" type="float" value="" size="3"
-                    label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
+                    label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help="(--yMin)"/>
                 <param name="yMax" type="float" value="" size="3"
-                    label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/>
+                    label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help="(--yMax)"/>
                 <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
-                    label="Description for the x-axis label" />
+                    label="Description for the x-axis label" help="(--xAxisLabel)"/>
                 <param name="yAxisLabel" type="text" value="genes" size="30"
-                    label="Description for the y-axis label for the top panel" />
+                    label="Description for the y-axis label for the top panel" help="(--yAxisLabel)"/>
 
                 <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."/>
@@ -150,7 +156,7 @@
                     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.">
+                    help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar. (--whatToShow)">
                     <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
                     <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
                     <option value="heatmap only">heatmap only</option>
@@ -160,17 +166,17 @@
 
                 <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;." />
+                    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;. (--startLabel)" />
                 <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)."/>
+                    help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site). (--endLabel)"/>
 
                 <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." />
+                    help ="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. (--referencePointLabel)" />
                 <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, label1, label2.">
+                    help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2. (--regionsLabel)">
                     <sanitizer>
                         <valid initial="string.printable">
                         </valid>
@@ -179,7 +185,8 @@
                 <expand macro="plotTitle" />
                 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 
                     label="Do one plot per group" 
-                    help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/>
+                    help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default.
+                        If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/>
 
                 <expand macro="kmeans_clustering" />
             </when>
@@ -192,7 +199,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" />
+            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
         </test>
     </tests>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b plotCorrelation.xml
--- a/plotCorrelation.xml	Mon May 25 05:16:10 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,195 +0,0 @@
-<tool id="deeptools_plotCorrelation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
-    <description>creates a heatmap for a score associated to genomic regions</description>
-    <macros>
-        <token name="@BINARY@">heatmapper</token>
-        <import>deepTools_macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <command>
-<![CDATA[
-        heatmapper
-
-        --matrixFile $matrixFile
-        --outFileName $outFileName
-
-        #if $output.showOutputSettings == "yes"
-            --plotFileFormat $output.outFileFormat
-            #if $outFileNameData:
-                --outFileNameData '$outFileNameData'
-            #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
-      
-            #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
-
-            --colorMap '$advancedOpt.colorMap'
-
-            #if str($advancedOpt.zMin).strip() != "":
-                --zMin $advancedOpt.zMin
-            #end if
-            #if $advancedOpt.zMax:
-                --zMax $advancedOpt.zMax
-            #end if
-
-            #if str($advancedOpt.yMin).strip() != "":
-                --yMin $advancedOpt.yMin
-            #end if
-            #if $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 $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
-                --plotTitle '$advancedOpt.plotTitle'
-            #end if
-
-            $advancedOpt.onePlotPerGroup
-
-            @KMEANS_CLUSTERING@
-
-        #end if
-]]>
-    </command>
-    <inputs>
-        <param name="corData" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
-
-        <expand macro="input_graphic_output_settings">
-            <expand macro="input_image_file_format" />
-            <expand macro="input_save_matrix_values" />
-        </expand>
-
-        <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">
-
-                <expand macro="colormap" />
-
-                <param name="zMin" type="float" value="" size="3"
-                    label="Minimum value for the heatmap intensities. Leave empty for automatic values"/>
-                <param name="zMax" type="float" value="" size="3"
-                    label="Maximum value for the heatmap intensities. Leave empty for automatic values"/>
-
-                <param name="yMin" type="float" value="" size="3"
-                    label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
-                <param name="yMax" type="float" value="" size="3"
-                    label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/>
-                <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="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 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="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;. (--startLabel)" />
-                <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. (--endLabel)"/>
-
-                <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 (--referencePointLabel)" />
-                <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, label1, label2. (--regionsLabel)">
-                    <sanitizer>
-                        <valid initial="string.printable">
-                        </valid>
-                    </sanitizer>
-                </param>
-
-                <expand macro="plotTitle" />
-                <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue=""
-                    label="Do one plot per group"
-                    help="When computeMatrix was used on more than one group of genes,
-                    the average plots for all the groups will be drawn in one panel by default.
-                    If this option is set, each group will get its own plot, stacked on top of each other. (--onePlotPerGroup)"/>
-
-                <expand macro="kmeans_clustering" />
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <expand macro="output_image_file_format" />
-        <expand macro="output_graphic_outputs" />
-        <expand macro="output_save_matrix_values" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" />
-            <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-**What it does**
-
-Tool for visualizing a correlation using either bamCorrelate or
-bigwigCorrelate. Pearson or Spearman methods are available to compute correlation
-coefficients. Results can be saved into a heat map image or as multiple
-scatter plots. Further output files are optional.
-
------
-
-@REFERENCES@
-]]>
-    </help>
-    <expand macro="citations" />
-</tool>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b profiler.xml
--- a/profiler.xml	Mon May 25 05:16:10 2015 -0400
+++ b/profiler.xml	Sat May 30 13:55:46 2015 -0400
@@ -168,7 +168,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" />
+            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
             <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="100" />
         </test>
     </tests>
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/1.bigwig
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/_1.bigwig
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/_2.bigwig
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/_3.bigwig
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/bamCorrelate_result1.png
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/bamFingerprint_result1.png
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/bamPEFragmentSize_histogram_result1.png
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/bigwigCompare_result1.bw
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/bigwigCompare_result2.bg
--- a/test-data/bigwigCompare_result2.bg	Mon May 25 05:16:10 2015 -0400
+++ b/test-data/bigwigCompare_result2.bg	Sat May 30 13:55:46 2015 -0400
@@ -1,5 +1,3 @@
-chr21	0	10000000	1.0
-chr21	10000000	20000000	1.0
-chr21	20000000	30000000	1.0
-chr21	30000000	40000000	1.0
-chr21	40000000	48129895	1.0
+ch1	0	400	1.0
+ch2	0	400	1.0
+ch3	0	400	1.0
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/bigwigCorrelate_result1.png
Binary file test-data/bigwigCorrelate_result1.png has changed
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/computeGCBias_result1.png
Binary file test-data/computeGCBias_result1.png has changed
diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/computeGCBias_result1.tabular
--- a/test-data/computeGCBias_result1.tabular	Mon May 25 05:16:10 2015 -0400
+++ b/test-data/computeGCBias_result1.tabular	Sat May 30 13:55:46 2015 -0400
@@ -1,12 +1,3 @@
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/correctGCBias_result1.bam
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/paired_chr2L.bam
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/sequence.2bit
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b test-data/test.bw
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diff -r 9bee2c86eeb1 -r 1dbd76a58d8b tool_dependencies.xml
--- a/tool_dependencies.xml	Mon May 25 05:16:10 2015 -0400
+++ b/tool_dependencies.xml	Sat May 30 13:55:46 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="deepTools" version="1.5.10">
-        <repository changeset_revision="41de4f005517" name="package_python_2_7_deeptools_1_5_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="54de6406521d" name="package_python_2_7_deeptools_1_5_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>