# HG changeset patch
# User iuc
# Date 1432545370 14400
# Node ID 9bee2c86eeb1ecc56e9e2d7e78bacd9e44ba27ae
# Parent  627004611e9882238ae08ac368f9eea0f9757cd0
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ab1ab06323702186cf0c883d5774720cbb822cb5-dirty

diff -r 627004611e98 -r 9bee2c86eeb1 bamCompare.xml
--- a/bamCompare.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/bamCompare.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_bamCompare" name="bamCompare" version="@WRAPPER_VERSION@.0">
     <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">bamCompare</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         bamCompare
@@ -71,7 +70,9 @@
             #if str($advancedOpt.ignoreForNormalization).strip() != '':
                 --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
             #end if
-
+            #if $samFlag:
+                --samFlag $samFlag
+            #end if
         #end if
 ]]>
     </command>
@@ -157,6 +158,7 @@
                 <param name="ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"
                     help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
+                <expand macro="samFlag" />
             </when>
         </conditional>
     </inputs>
diff -r 627004611e98 -r 9bee2c86eeb1 bamCorrelate.xml
--- a/bamCorrelate.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/bamCorrelate.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_bamCorrelate" name="bamCorrelate" version="@WRAPPER_VERSION@.0">
     <description>correlates pairs of BAM files</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">bamCorrelate</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         #set files=[]
@@ -19,8 +18,8 @@
 
         @THREADS@
 
-        --bamfiles #echo " ".join($files)
-        --labels #echo " ".join($labels)
+        --bamfiles '#echo "' '".join($files)#'
+        --labels '#echo "' '".join($labels)#'
         --fragmentLength $fragmentLength
         --corMethod $corMethod
 
@@ -29,7 +28,7 @@
         #if $output.showOutputSettings == "yes"
             --outRawCounts '$outFileRawCounts' 
             --outFileCorMatrix '$outFileCorMatrix'
-            --plotFileFormat $output.outFileFormat
+            --plotFileFormat '$output.outFileFormat'
         #else:
             --plotFileFormat 'png'
         #end if
@@ -38,7 +37,6 @@
             --binSize '$mode.binSize'
             --distanceBetweenBins '$mode.distanceBetweenBins'
             $mode.doNotRemoveOutliers
-
         #else:
             --BED $mode.region_file
         #end if
@@ -48,6 +46,10 @@
             --region '$mode.region'
         #end if
 
+        #if $plotTitle and str($plotTitle).strip() != "":
+            --plotTitle '$plotTitle'
+        #end if
+        $plotNumbers
         #if $mode.advancedOpt.showAdvancedOpt == "yes":
 
             $mode.advancedOpt.doNotExtendPairedEnds
@@ -75,7 +77,10 @@
 
         <param name="fragmentLength" type="integer" value="200" min="1"
             label="Length of the average fragment size"
-            help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length. (--fragmentLength)"/>
+            help ="Reads will be extended to match this length unless they are paired-end,
+            in which case they will be extended to match the fragment length.
+            *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will
+            be extended to match the fragment length. (--fragmentLength)"/>
 
         <param name="corMethod" type="select" label="Correlation method">
             <option value="spearman" selected="True">Spearman</option>
@@ -84,14 +89,18 @@
 
         <conditional name="mode">
             <param name="modeOpt" type="select" label="Choose computation mode" 
-                help="In the bins mode, the correlation is computed based on equal length bins. In the BED file mode, as list of genomic regions in BED format has to be given. For each region in the BED file the number of overlapping reads is counted in each of the BAM files. Then the correlation is computed.">
+                help="In the bins mode, the correlation is computed based on equal
+                length bins. In the BED file mode, as list of genomic regions in BED
+                format has to be given. For each region in the BED file the number of
+                overlapping reads is counted in each of the BAM files.
+                Then the correlation is computed.">
                 <option value="bins" selected="true">Bins</option>
                 <option value="BED-file">Limit correlation to certain regions (BED file)</option>
             </param>
             <when value="bins">
                 <param name="binSize" type="integer" value="10000" min="1" 
                     label="Bin size in bp"
-                    help="Length in base pairs for a window used to sample the genome."/>
+                    help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
 
                 <param name="distanceBetweenBins" type="integer" value="0" min="0"
                     label="Distance between bins"
@@ -99,7 +108,7 @@
                         the specified 'Bin size'. However, to reduce the
                         computation time, a larger distance between bins can
                         by given. Larger distances result in less bins being
-                        considered"/>
+                        considered. (--distanceBetweenBins)"/>
 
                 <param name="doNotRemoveOutliers" type="boolean"
                     truevalue="--doNotRemoveOutliers" falsevalue="" label="Do not filter outliers"
@@ -113,7 +122,7 @@
                         bamCorrelate tries to remove outliers using
                         the median absolute deviation (MAD) method applying a
                         threshold of 200 to only consider extremely large
-                        deviations from the median."/>
+                        deviations from the median. (--doNotRemoveOutliers)"/>
 
                 <expand macro="bamCorrelate_mode_actions" />
             </when>
@@ -124,7 +133,8 @@
                 <expand macro="bamCorrelate_mode_actions" />
             </when>
         </conditional>
-
+        <expand macro="plotTitle" />
+        <expand macro="plotNumbers" />
         <conditional name="output">
             <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                 <option value="no" selected="true">no</option>
@@ -162,9 +172,11 @@
         <test>
             <repeat name="input_files">
                 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
+                <param name="label" value="first BAM file" />
             </repeat>
             <repeat name="input_files">
                 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
+                <param name="label" value="second BAM file" />
             </repeat>
             <param name="modeOpt" value="bins" />
             <param name="binSize" value="10" />
diff -r 627004611e98 -r 9bee2c86eeb1 bamCoverage.xml
--- a/bamCoverage.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/bamCoverage.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_bamCoverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
     <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" />
     <macros>
         <token name="@BINARY@">bamCoverage</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         bamCoverage
@@ -53,7 +52,9 @@
                 ##if str($advancedOpt.ignoreForNormalization).strip() != '':
                 ##    --ignoreForNormalization $advancedOpt.ignoreForNormalization
                 ##end if
-
+                #if $samFlag:
+                    --samFlag $samFlag
+                #end if
             #end if
 ]]>
     </command>
@@ -109,9 +110,8 @@
                 <expand macro="doNotExtendPairedEnds" />
                 <expand macro="ignoreDuplicates" />
                 <expand macro="minMappingQuality" />
-
                 <expand macro="missingDataAsZero" />
-
+                <expand macro="samFlag" />
              <!--   <param name="ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"
                     help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
diff -r 627004611e98 -r 9bee2c86eeb1 bamFingerprint.xml
--- a/bamFingerprint.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/bamFingerprint.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0">
     <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">bamFingerprint</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         @multiple_input_bams@
@@ -19,8 +18,7 @@
 
             --fragmentLength $fragmentLength
 
-            #set newoutFileName=str($outFileName)+".png"
-            --plotFile $newoutFileName
+            --plotFile $outFileName
 
             #if $output.showOutputSettings == "yes"
                 --plotFileFormat $output.outFileFormat
@@ -46,9 +44,12 @@
                 #if $advancedOpt.minMappingQuality:
                 --minMappingQuality '$advancedOpt.minMappingQuality'
                 #end if
+
+                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
+                    --plotTitle '$advancedOpt.plotTitle'
+                #end if
+
             #end if
-        ; mv $newoutFileName $outFileName
-        ; rm $temp_dir -rf
 ]]>
     </command>
 
@@ -74,7 +75,7 @@
                 <expand macro="ignoreDuplicates" />
                 <expand macro="minMappingQuality" />
                 <expand macro="skipZeros" />
-
+                <expand macro="plotTitle" />
             </when>
         </conditional>
         <conditional name="output">
@@ -85,7 +86,7 @@
             <when value="no" />
             <when value="yes">
                 <expand macro="input_image_file_format" />
-                <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
+                <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
             </when>
         </conditional>
     </inputs>
diff -r 627004611e98 -r 9bee2c86eeb1 bamPEFragmentSize.xml
--- a/bamPEFragmentSize.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/bamPEFragmentSize.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
-    <description>Given a BAM file it samples several regions to estimate the paird-end fragment length</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
+    <description>Given a BAM file it samples several regions to estimate the paired-end fragment length</description>
     <macros>
         <token name="@BINARY@">bamPEFragmentSize</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         bamPEFragmentSize
@@ -16,8 +15,6 @@
             #end if
             '$bamInput'
             > $outfile
-        &&
-        mv ./hist.png $histogram_outfile
 ]]>
     </command>
     <inputs>
@@ -29,7 +26,7 @@
     </inputs>
     <outputs>
         <data name="outfile" format="txt"/>
-        <data name="histogram_outfile" format="png">
+        <data name="histogram_outfile" from_work_dir="hist.png" format="png">
             <filter>histogram is True</filter>
         </data>
     </outputs>
diff -r 627004611e98 -r 9bee2c86eeb1 bigwigCompare.xml
--- a/bigwigCompare.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/bigwigCompare.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_bigwigCompare" name="bigwigCompare" version="@WRAPPER_VERSION@.0">
     <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
-    <expand macro="requirements"/>
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">bigwigCompare</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements"/>
     <command>
 <![CDATA[
         bigwigCompare
@@ -34,6 +33,10 @@
           --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
           --binSize $advancedOpt.binSize
 
+            #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
+                --plotTitle '$advancedOpt.plotTitle'
+            #end if
+
         #end if
 ]]>
     </command>
@@ -80,8 +83,17 @@
                     help="Size of the bins in bp for the output of the bigwig/bedgraph file. (--binSize)"/>
                 <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
                     label ="Treat missing data as zero"
-                    help  ="This parameter determines if missing data should be replaced with a zero. If set to &quot;no&quot;, missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage. (--missingDataAsZero)" />
+                    help  ="This parameter determines if missing data should be replaced with a zero.
+                    If set to &quot;no&quot;, missing data will be ignored and will not be included in the
+                    output file at all. Missing data is defined as those regions for which no value exists in
+                    *any* of the bigwig files. The decision to include or exclude missing data depends on
+                    the interpretation of the data. Missing data in a bigwig file may mean that there is no
+                    information available for certain regions, for example a repetitive region that is not
+                    being considered. In the same file regions with low coverage may get zero read counts.
+                    If missing data is replaced by zero, this would convert the excluded repetitive regions
+                    into regions of low coverage. (--missingDataAsZero)" />
                 <expand macro="scaleFactor" />
+                <expand macro="plotTitle" />
             </when>
         </conditional>
     </inputs>
diff -r 627004611e98 -r 9bee2c86eeb1 bigwigCorrelate.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwigCorrelate.xml	Mon May 25 05:16:10 2015 -0400
@@ -0,0 +1,183 @@
+<tool id="deeptools_bamCorrelate" name="bigwigCorrelate" version="@WRAPPER_VERSION@.0">
+    <description>correlates pairs of BigWig files</description>
+    <macros>
+        <token name="@BINARY@">bigwigCorrelate</token>
+        <import>deepTools_macros.xml</import>
+    </macros> 
+   <expand macro="requirements" />
+    <command>
+<![CDATA[
+        #set files=[]
+        #set labels=[]
+
+        @multiple_input_bigwigs@
+
+        bigwigCorrelate
+
+        $mode.modeOpt
+
+        @THREADS@
+
+        --bwfiles '#echo "' '".join($files)#'
+        --labels '#echo "' '".join($labels)#'
+        #if $filterPercentile:
+            --filterPercentile $filterPercentile
+        #end if
+        --corMethod $corMethod
+
+        --plotFile $outFileName
+
+        #if $output.showOutputSettings == "yes"
+            --outRawCounts '$outFileRawCounts' 
+            --outFileCorMatrix '$outFileCorMatrix'
+            --plotFileFormat '$output.outFileFormat'
+        #else:
+            --plotFileFormat 'png'
+        #end if
+
+        #if $mode.modeOpt == "bins":
+            --binSize '$mode.binSize'
+        #else:
+            --BED $mode.region_file
+        #end if
+
+        #### options available in both modes
+        #if str($region.value) != '':
+            --region '$region'
+        #end if
+
+        #if $advancedOpt.showAdvancedOpt == "yes":
+
+            $advancedOpt.includeZeros
+
+            #if $advancedOpt.zMin:
+                --zMin $advancedOpt.zMin
+            #end if
+            #if $advancedOpt.zMax:
+                --zMax $advancedOpt.zMax
+            #end if
+            --colorMap '$advancedOpt.colorMap'
+
+            #if $plotTitle and str($plotTitle).strip() != "":
+                --plotTitle '$plotTitle'
+            #end if
+            $plotNumbers
+
+        #end if
+]]>
+    </command>
+
+    <inputs>
+        <expand macro="multiple_input_bigwigs" />
+
+        <param name="filterPercentile" type="float" optional="True" value="" min="0.0" max="100.0"
+            label="Percentile used to filter out extreme outliers"
+            help ="If not specified, it is automatically set to 99.9 in analyses
+                    using Pearson correlation! This means that values
+                    above that threshold, which consistently occur in all
+                    datasets, will not be taken into account for the
+                    correlation analysis. This behavior can be overridden
+                    by a user specified value from within the 0.0 to 100.0
+                    range. (--filterPercentile)"/>
+
+        <param name="corMethod" type="select" label="Correlation method" help="(--corMethod)">
+            <option value="spearman" selected="True">Spearman</option>
+            <option value="pearson">Pearson</option>
+        </param>
+
+        <conditional name="mode">
+            <param name="modeOpt" type="select" label="Choose computation mode" 
+                help="In the bins mode, the correlation is computed based on equal length bins.
+                In the BED file mode, as list of genomic regions in BED format has to be given.
+                For each region in the BED file the number of overlapping reads is counted in
+                each of the BAM files. Then the correlation is computed.">
+                <option value="bins" selected="true">Bins</option>
+                <option value="BED-file">Limit correlation to certain regions (BED file)</option>
+            </param>
+            <when value="bins">
+                <param name="binSize" type="integer" value="10000" min="1" 
+                    label="Bin size in bp"
+                    help="Length in base pairs for a window used to sample the genome. (--binSize)"/>
+            </when>
+            <when value="BED-file">
+                <param name="region_file" type="data" format="bed"
+                    label="Region file in BED format"
+                    help="Correlation is computed for the number of reads that overlap such regions."/>
+            </when>
+        </conditional>
+
+        <expand macro="bigwigCorrelate_mode_actions" />
+        <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"/>
+                <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <expand macro="output_image_file_format" />
+        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and 
+                output['saveRawCounts'] is True
+            ))
+            </filter>
+        </data>
+        <data format="tabular" name="outFileCorMatrix" label="${tool.name} on ${on_string}: correlation matrix">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and 
+                output['saveCorMatrix'] is True
+            ))
+            </filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <repeat name="input_files">
+                <param name="bigwigfile" value="1.bigwig" ftype="bigwig" />
+                <param name="label" value="first bigwig file" />
+            </repeat>
+            <repeat name="input_files">
+                <param name="bigwigfile" value="1.bigwig" 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" />
+            <output name="outFileName" file="bigwigCorrelate_result1.png" ftype="png" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+bigwigCorrelate computes the overall similarity between two or more bigWig
+files based on coverage means of genomic regions. The correlation analysis
+is performed for the entire genome by running the program in 'bins' mode,
+or for certain regions only in 'BED-file' mode. Pearson or Spearman analyses
+are available to compute correlation coefficients. Results are saved to a
+heat map file. Further output files are optional.
+
+
+**Output files**:
+
+- **diagnostic plot**: clustered heatmap displaying the values for each pair-wise correlation
+- data matrix (optional): if you want to plot the correlation values using a different program, e.g. R, this matrix can be used
+
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r 627004611e98 -r 9bee2c86eeb1 computeGCBias.xml
--- a/computeGCBias.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/computeGCBias.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_computeGCBias" name="computeGCBias" version="@WRAPPER_VERSION@.0">
     <description>to see whether your samples should be normalized for GC bias</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">computeGCBias</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         ln -s $bamInput local_bamInput.bam;
@@ -31,7 +30,6 @@
             #end if
 
             #if $advancedOpt.showAdvancedOpt == "yes":
-
                 --sampleSize '$advancedOpt.sampleSize'
                 --regionSize '$advancedOpt.regionSize'
 
@@ -70,10 +68,17 @@
                     label="Number of sampling points to be considered" help="(--sampleSize)" />
                 <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. (--regionSize)"/>
+                    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. (--regionSize)"/>
                 <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. (--filterOut)" />
+                    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. (--filterOut)" />
                 <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="(--extraSampling)" />
diff -r 627004611e98 -r 9bee2c86eeb1 computeMatrix.xml
--- a/computeMatrix.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/computeMatrix.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,32 +1,27 @@
 <tool id="deeptools_computeMatrix" name="computeMatrix" version="@WRAPPER_VERSION@.0">
-    <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
+    <description>preparation step to plot a heatmap or a profile</description>
     <macros>
         <token name="@BINARY@">computeMatrix</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         #import tempfile
 
-        #set $temp_input_handle = tempfile.NamedTemporaryFile()
-        #set $temp_input_path = $temp_input_handle.name
-        #silent $temp_input_handle.close()
-
         #for $rf in $regionsFiles:
-            cat "$rf.regionsFile" >> $temp_input_path;
+            cat "$rf.regionsFile" >> ./temp_input_path;
             #if str($rf.label.value).strip():
-                echo "\#$rf.label.value" >> $temp_input_path;
+                echo "\#$rf.label.value" >> ./temp_input_path;
             #else:
-                echo "\#$rf.regionsFile.name" >> $temp_input_path;
+                echo "\#$rf.regionsFile.name" >> ./temp_input_path;
             #end if
         #end for
 
         computeMatrix
 
             $mode.mode_select
-            --regionsFileName '$temp_input_path'
+            --regionsFileName ./temp_input_path
             --scoreFileName '$scoreFile'
             --outFileName '$outFileName'
 
@@ -79,24 +74,33 @@
                 #end if
 
             #end if
-        ; rm $temp_input_path
 ]]>
     </command>
     <inputs>
 
         <repeat name="regionsFiles" title="regions to plot" min="1">
-            <param name="regionsFile" format="bed" type="data" label="Regions to plot" help="File, in BED format, containing the regions to plot."/>
-            <param name="label" type="text" size="30" optional="true" value="" label="Label" help="Label to use in the output."/>
+            <param name="regionsFile" format="bed" type="data" label="Regions to plot"
+                help="File, in BED format, containing the regions to plot."/>
+            <param name="label" type="text" size="30" optional="true" value="" label="Label"
+                help="Label to use in the output."/>
         </repeat>
 
         <param name="scoreFile" format="bigwig" type="data"
             label="Score file"
-            help="Should be a bigWig file (containing a score, usually covering the whole genome). You can generate a bigWig file either from a bedGraph or WIG file using UCSC tools or from a BAM file using the deepTool bamCoverage. (-scoreFile)"/>
+            help="Should be a bigWig file (containing a score, usually covering
+            the whole genome). You can generate a bigWig file either from a
+            bedGraph or WIG file using UCSC tools or from a BAM file using the
+            deepTool bamCoverage. (-scoreFile)"/>
 
         <conditional name="mode" >
             <param name="mode_select" type="select"
                 label="computeMatrix has two main output options"
-                help="In the scale-regions mode, all regions in the BED file are stretched or shrunk to the same length (bp) that is indicated by the user. Reference-point refers to a position within the BED regions (e.g start of region). In the reference-point mode only those genomic positions before (downstream) and/or after (upstream) the reference point will be plotted.">
+                help="In the scale-regions mode, all regions in the BED file are
+                stretched or shrunk to the same length (bp) that is indicated
+                by the user. Reference-point refers to a position within the BED
+                regions (e.g start of region). In the reference-point mode only
+                those genomic positions before (downstream) and/or after (upstream)
+                the reference point will be plotted.">
                 <option value="scale-regions" selected="true">scale-regions</option>
                 <option value="reference-point">reference-point</option>
             </param>
@@ -106,7 +110,9 @@
                     label="Distance in bp to which all regions are going to be fitted" help="(--regionBodyLength)"/>
                 <param name="startLabel" type="text" value="TSS" size="10"
                     label="Label for the region start"
-                    help ="Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;. (--startLabel)" />
+                    help ="Label shown in the plot for the start of the region.
+                    Default is TSS (transcription start site), but could be changed to anything,
+                    e.g. &quot;peak start&quot;. (--startLabel)" />
                 <param name="endLabel" type="text" value="TES" size="10"
                     label="Label for the region end"
                     help="Label shown in the plot for the region end. Default is TES (transcription end site). (--endLabel)"/>
@@ -119,10 +125,12 @@
                     <when value="yes">
                         <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. (--beforeRegionStartLength)"/>
+                            help="If the regions are genes, this would be the
+                            distance upstream of the transcription start site. (--beforeRegionStartLength)"/>
                         <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. (--afterRegionStartLength)"/>
+                            help="If the regions are genes, this would be the
+                            distance downstream of the transcription end site. (--afterRegionStartLength)"/>
                     </when>
                 </conditional>
             </when>
@@ -134,7 +142,8 @@
                 </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. (--nanAfterEnd)"/>
+                    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. (--nanAfterEnd)"/>
                 <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. (--beforeRegionStartLength)"/>
@@ -188,23 +197,33 @@
 
                 <param name="missingDataAsZero" type="boolean" truevalue="--missingDataAsZero" falsevalue=""
                     label="Indicate missing data as zero"
-                    help="Set to &quot;yes&quot;, if missing data should be indicated as zeros. Default is to ignore such cases which will be depicted as black areas in the heatmap. (see &quot;Missing data color&quot; options of the heatmapper for additional options). (--missingDataAsZero)"/>
+                    help="Set to &quot;yes&quot;, if missing data should be indicated as zeros.
+                    Default is to ignore such cases which will be depicted as black areas in the
+                    heatmap. (see &quot;Missing data color&quot; options of the heatmapper for additional options).
+                    (--missingDataAsZero)"/>
                 <param name="skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
                     label="Skip zeros"
-                    help="Whether regions with only scores of zero should be included or not. Default is to include them. (--skipZeros)"/>
+                    help="Whether regions with only scores of zero should be included or not.
+                    Default is to include them. (--skipZeros)"/>
                 <param name="minThreshold" type="float" optional="True"
                     label="Minimum threshold"
-                    help="Any region containing a value that is equal or less than this numeric value will be skipped. This is useful to skip, for example, genes where the read count is zero for any of the bins. This could be the result of unmappable areas and can bias the overall results. (--minThreshold)"/>
+                    help="Any region containing a value that is equal or less than this numeric
+                    value will be skipped. This is useful to skip, for example, genes where the
+                    read count is zero for any of the bins. This could be the result of
+                    unmappable areas and can bias the overall results. (--minThreshold)"/>
                 <param name="maxThreshold" type="float" optional="True"
                     label="Maximum threshold"
-                    help="Any region containing a value that is equal or higher that this numeric value will be skipped. The max threshold is useful to skip those few regions with very high read counts (e.g. major satellites) that may bias the average values. (--maxThreshold)"/>
+                    help="Any region containing a value that is equal or higher that this
+                    numeric value will be skipped. The max threshold is useful to skip those
+                    few regions with very high read counts (e.g. major satellites) that may
+                    bias the average values. (--maxThreshold)"/>
                 <param name="scale" type="float" optional="True" label="Scaling factor"
                     help="If set, all values are multiplied by this number. (--scale)"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
+        <data format="deeptools_matrix" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
         <expand macro="output_graphic_outputs" />
         <expand macro="output_save_matrix_values" />
     </outputs>
@@ -223,7 +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="bgzip" compare="sim_size" />
+            <output name="outFileName" file="computeMatrix_result1.gz" ftype="deeptools_matrix" compare="sim_size" />
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
@@ -233,7 +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="bgzip" compare="sim_size" />
+            <output name="outFileName" file="computeMatrix_result2.gz" ftype="deeptools_matrix" compare="sim_size" />
         </test>
     </tests>
   <help>
diff -r 627004611e98 -r 9bee2c86eeb1 correctGCBias.xml
--- a/correctGCBias.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/correctGCBias.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_correctGCBias" name="correctGCBias" version="@WRAPPER_VERSION@.0">
     <description>uses the output from computeGCBias to generate corrected BAM files</description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">correctGCBias</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         ln -s $bamInput local_bamInput.bam;
@@ -33,7 +32,7 @@
     <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."/>
+            label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted. (--bamfile)" />
         <expand macro="reference_genome_source" />
         <expand macro="effectiveGenomeSize" />
         <expand macro="region_limit_operation" />
diff -r 627004611e98 -r 9bee2c86eeb1 deepTools_macros.xml
--- a/deepTools_macros.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/deepTools_macros.xml	Mon May 25 05:16:10 2015 -0400
@@ -13,23 +13,53 @@
                 <expand macro="doNotExtendPairedEnds" />
                 <expand macro="ignoreDuplicates" />
                 <expand macro="minMappingQuality" />
-                <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
-                    label="Include zeros"
-                    help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" />
-                <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
-                    help="If not specified the value is set automatically. (--zMin)"/>
-                <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
-                    help="If not specified the value is set automatically. (--zMax)"/>
+                <expand macro="includeZeros" />
+                <expand macro="zMin_zMax" />
                 <expand macro="colormap" />
             </when>
         </conditional>
     </xml>
 
+
+    <xml name="bigwigCorrelate_mode_actions">
+
+        <expand macro="region_limit_operation" />
+
+        <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="includeZeros" />
+                <expand macro="zMin_zMax" />
+                <expand macro="colormap" />
+                <expand macro="plotTitle" />
+                <expand macro="plotNumbers" />
+            </when>
+        </conditional>
+    </xml>
+
+
+    <xml name="includeZeros">
+        <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
+            label="Include zeros"
+            help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases. (--includeZeros)" />
+    </xml>
+    <xml name="zMin_zMax">
+        <param name="zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
+            help="If not specified the value is set automatically. (--zMin)"/>
+        <param name="zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
+            help="If not specified the value is set automatically. (--zMax)"/>
+    </xml>
+
     <xml name="region_limit_operation">
         <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;. (--region)" />
     </xml>
+
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
     <token name="@WRAPPER_VERSION@">1.5.9.2</token>
     <xml name="requirements">
@@ -39,6 +69,7 @@
             <requirement type="package" version="1.5.9">deepTools</requirement>
             <yield />
         </requirements>
+        <expand macro="stdio" />
         <version_command>@BINARY@ --version</version_command>
     </xml>
 
@@ -77,6 +108,16 @@
         #end if
     </token>
 
+    <xml name="samFlag">
+        <param name="samFlag" type="integer" optional="true" value=""
+            label="Filter reads based on the SAM flag"
+            help= "For example to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage. (--samFlag)"/>
+    </xml>
+    <xml name="plotNumbers">
+        <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" 
+            label="Plot the correlation value" 
+            help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
+    </xml>
     <xml name="doNotExtendPairedEnds">
         <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
             label="Do not extend paired ends"
@@ -141,11 +182,6 @@
 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
 .. _help site: https://github.com/fidelram/deepTools/wiki/
 
-**References**
-
-If you use this Galaxy tool in work leading to a scientific publication please
-cite the following paper:
-
     </token>
     <xml name="citations">
         <citations>
@@ -162,7 +198,24 @@
             <param name="label" type="text" size="30" optional="true" value=""
                 label="Label"
                 help="Label to use in the output. If not given the dataset name will be used instead."/>
-          </repeat>
+        </repeat>
+    </xml>
+
+    <xml name="multiple_input_bigwigs">
+        <repeat name="input_files" title="BigWig files" min="2">
+            <param name="bigwigfile" type="data" format="bigwig" 
+                label="Bigwig file" 
+                help="The Bigwig file must be sorted."/>
+            <param name="label" type="text" size="30" optional="true" value=""
+                label="Label"
+                help="Label to use in the output. If not given the dataset name will be used instead."/>
+        </repeat>
+    </xml>
+
+    <xml name="plotTitle">
+        <param name="plotTitle" type="text" value="" size="30" optional="True"
+            label="Title of the plot"
+            help="Title of the plot, to be printed on top of the generated image. (--plotTitle)" />
     </xml>
 
     <token name="@multiple_input_bams@">
@@ -187,6 +240,27 @@
         #end for
     </token>
 
+    <token name="@multiple_input_bigwigs@">
+        #import tempfile
+        #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
+        #set files=[]
+        #set labels=[]
+        #for $i in $input_files:
+            #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
+            #set $temp_input_path = $temp_input_handle.name
+            #silent $temp_input_handle.close()
+            #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path))
+            #silent $files.append('%s.bw' % $temp_input_path)
+
+            ##set $files += [str($i.bigwigfile)]
+            #if str($i.label.value) != "":
+                #set $labels += ["\"%s\"" % ($i.label.value)]
+            #else
+                #set $labels += ["\"%s\"" % ($i.bigwigfile.name)]
+            #end if
+        #end for
+    </token>
+
     <xml name="reference_genome_source">
         <conditional name="source">
             <param name="ref_source" type="select" label="Reference genome">
diff -r 627004611e98 -r 9bee2c86eeb1 heatmapper.xml
--- a/heatmapper.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/heatmapper.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_heatmapper" name="heatmapper" version="@WRAPPER_VERSION@.0">
     <description>creates a heatmap for a score associated to genomic regions</description>
-    <expand macro="requirements"/>
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">heatmapper</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements"/>
     <command>
 <![CDATA[
         heatmapper
@@ -76,7 +75,7 @@
             --refPointLabel '$advancedOpt.referencePointLabel'
             --regionsLabel '$advancedOpt.regionsLabel'
 
-            #if str($advancedOpt.plotTitle.value) != "None":
+            #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                 --plotTitle '$advancedOpt.plotTitle'
             #end if
 
@@ -177,8 +176,7 @@
                         </valid>
                     </sanitizer>
                 </param>
-                <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. (--plotTitle)" />
+                <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."/>
@@ -194,7 +192,7 @@
     </outputs>
     <tests>
         <test>
-            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" />
+            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" />
             <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
         </test>
     </tests>
diff -r 627004611e98 -r 9bee2c86eeb1 plotCorrelation.xml
--- a/plotCorrelation.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/plotCorrelation.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,11 +1,10 @@
 <tool id="deeptools_plotCorrelation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
     <description>creates a heatmap for a score associated to genomic regions</description>
-    <expand macro="requirements"/>
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">heatmapper</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements"/>
     <command>
 <![CDATA[
         heatmapper
@@ -76,7 +75,7 @@
             --refPointLabel '$advancedOpt.referencePointLabel'
             --regionsLabel '$advancedOpt.regionsLabel'
 
-            #if str($advancedOpt.plotTitle.value) != "None":
+            #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
                 --plotTitle '$advancedOpt.plotTitle'
             #end if
 
@@ -110,13 +109,6 @@
                 <param name="zMax" type="float" value="" size="3"
                     label="Maximum value for the heatmap intensities. Leave empty for automatic values"/>
 
-                <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" 
-                    label="Plot the correlation value" 
-                    help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
-
-
-
-
                 <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"
@@ -142,27 +134,33 @@
 
                 <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. (--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 ="[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.">
+                    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>
-                <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. (--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."/>
+
+                <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>
diff -r 627004611e98 -r 9bee2c86eeb1 profiler.xml
--- a/profiler.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/profiler.xml	Mon May 25 05:16:10 2015 -0400
@@ -2,12 +2,11 @@
     <description>
         creates a profile plot for a score associated to genomic regions
     </description>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
     <macros>
         <token name="@BINARY@">profiler</token>
         <import>deepTools_macros.xml</import>
     </macros>
+    <expand macro="requirements" />
     <command>
 <![CDATA[
         profiler
@@ -44,7 +43,7 @@
 
             --regionsLabel '$advancedOpt.regionsLabel'
 
-            #if str($advancedOpt.plotTitle).strip() != "":
+            #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
                 --plotTitle '$advancedOpt.plotTitle'
             #end if
 
@@ -82,7 +81,9 @@
             <when value="yes">
                 <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;." />
                 <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)."/>
@@ -115,7 +116,14 @@
                     label="Plot width" 
                     help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
                 <param name="plotType" type="select" label="Plot type"
-                    help="For the summary plot (profile) only. The &quot;lines&quot; option will plot the profile line based on the average type selected. The &quot;fill&quot; option fills the region between zero and the profile curve. The fill in color is semi transparent to distinguish different profiles. The &quot;add standard error&quot; option colors the region between the profile and the standard error of the data. As in the case of fill, a semi-transparent color is used. The option &quot;overlapped_lines&quot; plots each region values, one on top of the other; this option only works if &quot;one plot per proup&quot; is set.">
+                    help="For the summary plot (profile) only. The &quot;lines&quot; option will
+                    plot the profile line based on the average type selected. The &quot;fill&quot;
+                    option fills the region between zero and the profile curve. The fill in color is
+                    semi transparent to distinguish different profiles. The &quot;add standard error&quot;
+                    option colors the region between the profile and the standard error of the data.
+                    As in the case of fill, a semi-transparent color is used.
+                    The option &quot;overlapped_lines&quot; plots each region values, one on top of
+                    the other; this option only works if &quot;one plot per proup&quot; is set.">
                     <option value="lines" selected="true">lines</option>
                     <option value="fill">fill</option>
                     <option value="se">add standard error</option>
@@ -123,20 +131,23 @@
                 </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." />
+                    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;."/>
+
+                <expand macro="plotTitle" />
                 <param name="colors" type="text" value="" size="40"
                     label="List of colors to use for the plotted lines"
-                    help="Color names and html hex strings (e.g. #eeff22) are accepted. The color names should be given separated by spaces. (--colors red blue green)">
+                    help="Color names and html hex strings (e.g. #eeff22) are accepted.
+                    The color names should be given separated by spaces. (--colors red blue green)">
                     <validator type="expression"
                         message="Only numbers, digits, '#' and spaces are allowed.">all(c in ' #abcdefghijklmnopqrstuvwxyz0123456789' for c in value)</validator>
                 </param>
 
                 <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."/>
+                    help="When the region file contains groups separated by &quot;#&quot;, the default is
+                    to plot the averages for the distinct plots in one plot. If this option is set, each group
+                    will get its own plot, stacked on top of each other."/>
                 <param name="yMin" type="float" value="" size="3" optional="true"
                     label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
                 <param name="yMax" type="float" value="" size="3" optional="true"
@@ -155,8 +166,15 @@
         <expand macro="output_image_file_format" />
         <expand macro="output_graphic_outputs" />
     </outputs>
+    <tests>
+        <test>
+            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_matrix" />
+            <output name="outFileName" file="profiler_result1.png" ftype="png" compare="sim_size" delta="100" />
+        </test>
+    </tests>
     <help>
 <![CDATA[
+
 **What it does**
 
 This tool plots the average enrichments over all genomic
diff -r 627004611e98 -r 9bee2c86eeb1 test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 627004611e98 -r 9bee2c86eeb1 test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 627004611e98 -r 9bee2c86eeb1 test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Sun Mar 22 13:02:33 2015 -0400
+++ b/test-data/bamCoverage_result3.bg	Mon May 25 05:16:10 2015 -0400
@@ -1,12 +1,11 @@
-chrM	0	210	8173200.00
-chrM	210	220	7999302.13
-chrM	220	230	7129812.77
-chrM	230	240	5564731.91
-chrM	240	250	4173548.94
-chrM	250	260	2434570.21
-chrM	260	300	1912876.60
-chrM	300	16310	1738978.72
-chrM	16310	16320	1565080.85
-chrM	16320	16330	869489.36
-chrM	16330	16340	695591.49
-chrM	16340	16350	347795.74
+chrM	0	210	12259800.00
+chrM	210	220	11998953.19
+chrM	220	230	10694719.15
+chrM	230	240	8347097.87
+chrM	240	250	6260323.40
+chrM	250	260	3391008.51
+chrM	260	16310	2608468.09
+chrM	16310	16320	2347621.28
+chrM	16320	16330	1304234.04
+chrM	16330	16340	1043387.23
+chrM	16340	16350	521693.62
diff -r 627004611e98 -r 9bee2c86eeb1 test-data/bamCoverage_result4.bg
--- a/test-data/bamCoverage_result4.bg	Sun Mar 22 13:02:33 2015 -0400
+++ b/test-data/bamCoverage_result4.bg	Mon May 25 05:16:10 2015 -0400
@@ -1,456 +1,460 @@
-phiX174	0	10	3742.31
-phiX174	10	20	18711.54
-phiX174	20	70	63619.23
-phiX174	70	90	82330.77
-phiX174	90	100	101042.31
-phiX174	100	120	104784.62
-phiX174	120	140	119753.85
-phiX174	140	160	138465.38
-phiX174	160	170	153434.62
-phiX174	170	180	183373.08
-phiX174	180	200	202084.62
-phiX174	200	210	205826.92
-phiX174	210	220	224538.46
-phiX174	220	230	265703.85
-phiX174	230	240	295642.31
-phiX174	240	250	303126.92
-phiX174	250	260	318096.15
-phiX174	260	270	366746.15
-phiX174	270	280	404169.23
-phiX174	280	290	419138.46
-phiX174	290	310	437850.00
-phiX174	310	320	456561.54
-phiX174	320	330	479015.38
-phiX174	330	350	497726.92
-phiX174	350	360	505211.54
-phiX174	360	370	508953.85
-phiX174	370	380	523923.08
-phiX174	380	400	550119.23
-phiX174	400	410	553861.54
-phiX174	410	420	550119.23
-phiX174	420	430	565088.46
-phiX174	430	440	583800.00
-phiX174	440	450	595026.92
-phiX174	450	460	609996.15
-phiX174	460	480	643676.92
-phiX174	480	490	658646.15
-phiX174	490	500	669873.08
-phiX174	500	510	673615.38
-phiX174	510	520	669873.08
-phiX174	520	530	684842.31
-phiX174	530	540	677357.69
-phiX174	540	550	707296.15
-phiX174	550	560	684842.31
-phiX174	560	570	711038.46
-phiX174	570	580	707296.15
-phiX174	580	600	699811.54
-phiX174	600	610	673615.38
-phiX174	610	620	722265.38
-phiX174	620	630	740976.92
-phiX174	630	640	722265.38
-phiX174	640	660	718523.08
-phiX174	660	670	711038.46
-phiX174	670	680	692326.92
-phiX174	680	690	733492.31
-phiX174	690	700	752203.85
-phiX174	700	710	737234.62
-phiX174	710	720	740976.92
-phiX174	720	730	759688.46
-phiX174	730	740	748461.54
-phiX174	740	750	759688.46
-phiX174	750	760	733492.31
-phiX174	760	770	714780.77
-phiX174	770	800	755946.15
-phiX174	800	810	744719.23
-phiX174	810	820	740976.92
-phiX174	820	830	726007.69
-phiX174	830	850	711038.46
-phiX174	850	860	729750.00
-phiX174	860	870	733492.31
-phiX174	870	880	722265.38
-phiX174	880	890	740976.92
-phiX174	890	900	748461.54
-phiX174	900	910	767173.08
-phiX174	910	920	759688.46
-phiX174	920	930	774657.69
-phiX174	930	940	770915.38
-phiX174	940	960	744719.23
-phiX174	960	970	714780.77
-phiX174	970	980	684842.31
-phiX174	980	990	692326.92
-phiX174	990	1000	677357.69
-phiX174	1000	1010	681100.00
-phiX174	1010	1020	722265.38
-phiX174	1020	1030	699811.54
-phiX174	1030	1040	744719.23
-phiX174	1040	1050	759688.46
-phiX174	1050	1060	763430.77
-phiX174	1060	1080	793369.23
-phiX174	1080	1100	785884.62
-phiX174	1100	1110	770915.38
-phiX174	1110	1130	767173.08
-phiX174	1130	1140	763430.77
-phiX174	1140	1160	797111.54
-phiX174	1160	1170	793369.23
-phiX174	1170	1190	804596.15
-phiX174	1190	1200	789626.92
-phiX174	1200	1210	782142.31
-phiX174	1210	1220	812080.77
-phiX174	1220	1230	797111.54
-phiX174	1230	1240	778400.00
-phiX174	1240	1250	748461.54
-phiX174	1250	1260	740976.92
-phiX174	1260	1270	759688.46
-phiX174	1270	1280	748461.54
-phiX174	1280	1290	763430.77
-phiX174	1290	1300	755946.15
-phiX174	1300	1310	737234.62
-phiX174	1310	1320	767173.08
-phiX174	1320	1330	755946.15
-phiX174	1330	1340	770915.38
-phiX174	1340	1350	778400.00
-phiX174	1350	1360	789626.92
-phiX174	1360	1370	812080.77
-phiX174	1370	1380	819565.38
-phiX174	1380	1390	778400.00
-phiX174	1390	1400	740976.92
-phiX174	1400	1410	770915.38
-phiX174	1410	1430	778400.00
-phiX174	1430	1440	793369.23
-phiX174	1440	1450	808338.46
-phiX174	1450	1460	830792.31
-phiX174	1460	1470	819565.38
-phiX174	1470	1480	804596.15
-phiX174	1480	1490	800853.85
-phiX174	1490	1500	785884.62
-phiX174	1500	1510	770915.38
-phiX174	1510	1520	759688.46
-phiX174	1520	1530	755946.15
-phiX174	1530	1540	770915.38
-phiX174	1540	1550	755946.15
-phiX174	1550	1560	778400.00
-phiX174	1560	1580	782142.31
-phiX174	1580	1590	718523.08
-phiX174	1590	1600	692326.92
-phiX174	1600	1620	651161.54
-phiX174	1620	1630	647419.23
-phiX174	1630	1640	684842.31
-phiX174	1640	1650	688584.62
-phiX174	1650	1660	692326.92
-phiX174	1660	1670	699811.54
-phiX174	1670	1680	714780.77
-phiX174	1680	1690	696069.23
-phiX174	1690	1710	707296.15
-phiX174	1710	1720	733492.31
-phiX174	1720	1730	740976.92
-phiX174	1730	1740	744719.23
-phiX174	1740	1750	729750.00
-phiX174	1750	1760	703553.85
-phiX174	1760	1770	696069.23
-phiX174	1770	1780	677357.69
-phiX174	1780	1790	666130.77
-phiX174	1790	1800	669873.08
-phiX174	1800	1810	677357.69
-phiX174	1810	1820	658646.15
-phiX174	1820	1830	707296.15
-phiX174	1830	1840	800853.85
-phiX174	1840	1850	819565.38
-phiX174	1850	1860	812080.77
-phiX174	1860	1870	830792.31
-phiX174	1870	1890	827050.00
-phiX174	1890	1900	830792.31
-phiX174	1900	1910	823307.69
-phiX174	1910	1920	812080.77
-phiX174	1920	1930	856988.46
-phiX174	1930	1940	875700.00
-phiX174	1940	1950	838276.92
-phiX174	1950	1960	853246.15
-phiX174	1960	1970	860730.77
-phiX174	1970	1980	886926.92
-phiX174	1980	2000	856988.46
-phiX174	2000	2010	886926.92
-phiX174	2010	2020	871957.69
-phiX174	2020	2030	875700.00
-phiX174	2030	2040	879442.31
-phiX174	2040	2050	883184.62
-phiX174	2050	2060	808338.46
-phiX174	2060	2070	804596.15
-phiX174	2070	2080	785884.62
-phiX174	2080	2090	819565.38
-phiX174	2090	2100	815823.08
-phiX174	2100	2110	819565.38
-phiX174	2110	2120	782142.31
-phiX174	2120	2130	800853.85
-phiX174	2130	2140	785884.62
-phiX174	2140	2160	770915.38
-phiX174	2160	2170	755946.15
-phiX174	2170	2180	737234.62
-phiX174	2180	2190	729750.00
-phiX174	2190	2200	711038.46
-phiX174	2200	2210	722265.38
-phiX174	2210	2220	718523.08
-phiX174	2220	2230	763430.77
-phiX174	2230	2250	770915.38
-phiX174	2250	2260	774657.69
-phiX174	2260	2280	744719.23
-phiX174	2280	2290	748461.54
-phiX174	2290	2300	752203.85
-phiX174	2300	2310	812080.77
-phiX174	2310	2320	842019.23
-phiX174	2320	2330	860730.77
-phiX174	2330	2340	845761.54
-phiX174	2340	2350	853246.15
-phiX174	2350	2360	849503.85
-phiX174	2360	2370	871957.69
-phiX174	2370	2380	860730.77
-phiX174	2380	2390	842019.23
-phiX174	2390	2400	860730.77
-phiX174	2400	2410	815823.08
-phiX174	2410	2420	819565.38
-phiX174	2420	2440	789626.92
-phiX174	2440	2450	785884.62
-phiX174	2450	2460	853246.15
-phiX174	2460	2470	883184.62
-phiX174	2470	2510	928092.31
-phiX174	2510	2520	871957.69
-phiX174	2520	2530	886926.92
-phiX174	2530	2540	916865.38
-phiX174	2540	2560	879442.31
-phiX174	2560	2570	875700.00
-phiX174	2570	2580	916865.38
-phiX174	2580	2590	924350.00
-phiX174	2590	2600	928092.31
-phiX174	2600	2610	909380.77
-phiX174	2610	2620	905638.46
-phiX174	2620	2630	901896.15
-phiX174	2630	2640	946803.85
-phiX174	2640	2650	935576.92
-phiX174	2650	2660	939319.23
-phiX174	2660	2670	943061.54
-phiX174	2670	2680	961773.08
-phiX174	2680	2690	943061.54
-phiX174	2690	2700	928092.31
-phiX174	2700	2710	920607.69
-phiX174	2710	2720	950546.15
-phiX174	2720	2730	969257.69
-phiX174	2730	2740	984226.92
-phiX174	2740	2760	1025392.31
-phiX174	2760	2770	999196.15
-phiX174	2770	2780	987969.23
-phiX174	2780	2790	1006680.77
-phiX174	2790	2810	991711.54
-phiX174	2810	2820	961773.08
-phiX174	2820	2830	931834.62
-phiX174	2830	2840	939319.23
-phiX174	2840	2850	909380.77
-phiX174	2850	2860	894411.54
-phiX174	2860	2870	909380.77
-phiX174	2870	2880	928092.31
-phiX174	2880	2890	913123.08
-phiX174	2890	2900	886926.92
-phiX174	2900	2910	894411.54
-phiX174	2910	2920	868215.38
-phiX174	2920	2930	853246.15
-phiX174	2930	2940	815823.08
-phiX174	2940	2950	864473.08
-phiX174	2950	2960	860730.77
-phiX174	2960	2970	864473.08
-phiX174	2970	2980	875700.00
-phiX174	2980	2990	856988.46
-phiX174	2990	3000	871957.69
-phiX174	3000	3010	901896.15
-phiX174	3010	3020	871957.69
-phiX174	3020	3030	883184.62
-phiX174	3030	3040	864473.08
-phiX174	3040	3050	834534.62
-phiX174	3050	3060	879442.31
-phiX174	3060	3070	890669.23
-phiX174	3070	3090	886926.92
-phiX174	3090	3100	871957.69
-phiX174	3100	3110	916865.38
-phiX174	3110	3120	901896.15
-phiX174	3120	3140	886926.92
-phiX174	3140	3160	898153.85
-phiX174	3160	3170	909380.77
-phiX174	3170	3190	913123.08
-phiX174	3190	3200	898153.85
-phiX174	3200	3220	879442.31
-phiX174	3220	3230	868215.38
-phiX174	3230	3240	886926.92
-phiX174	3240	3250	864473.08
-phiX174	3250	3260	845761.54
-phiX174	3260	3270	875700.00
-phiX174	3270	3280	890669.23
-phiX174	3280	3290	879442.31
-phiX174	3290	3300	853246.15
-phiX174	3300	3310	871957.69
-phiX174	3310	3320	856988.46
-phiX174	3320	3330	901896.15
-phiX174	3330	3340	909380.77
-phiX174	3340	3350	920607.69
-phiX174	3350	3360	935576.92
-phiX174	3360	3370	920607.69
-phiX174	3370	3380	935576.92
-phiX174	3380	3390	950546.15
-phiX174	3390	3410	905638.46
-phiX174	3410	3430	894411.54
-phiX174	3430	3440	909380.77
-phiX174	3440	3460	946803.85
-phiX174	3460	3470	976742.31
-phiX174	3470	3480	946803.85
-phiX174	3480	3490	961773.08
-phiX174	3490	3500	1006680.77
-phiX174	3500	3510	999196.15
-phiX174	3510	3530	1032876.92
-phiX174	3530	3540	991711.54
-phiX174	3540	3550	1010423.08
-phiX174	3550	3560	980484.62
-phiX174	3560	3570	965515.38
-phiX174	3570	3580	939319.23
-phiX174	3580	3600	935576.92
-phiX174	3600	3610	946803.85
-phiX174	3610	3630	916865.38
-phiX174	3630	3640	886926.92
-phiX174	3640	3650	879442.31
-phiX174	3650	3670	894411.54
-phiX174	3670	3690	898153.85
-phiX174	3690	3700	856988.46
-phiX174	3700	3710	868215.38
-phiX174	3710	3720	864473.08
-phiX174	3720	3730	875700.00
-phiX174	3730	3750	856988.46
-phiX174	3750	3760	849503.85
-phiX174	3760	3780	834534.62
-phiX174	3780	3790	808338.46
-phiX174	3790	3800	755946.15
-phiX174	3800	3810	711038.46
-phiX174	3810	3820	707296.15
-phiX174	3820	3830	658646.15
-phiX174	3830	3840	677357.69
-phiX174	3840	3850	692326.92
-phiX174	3850	3860	718523.08
-phiX174	3860	3870	722265.38
-phiX174	3870	3890	707296.15
-phiX174	3890	3900	692326.92
-phiX174	3900	3910	666130.77
-phiX174	3910	3920	636192.31
-phiX174	3920	3930	602511.54
-phiX174	3930	3940	591284.62
-phiX174	3940	3960	606253.85
-phiX174	3960	3970	621223.08
-phiX174	3970	3980	636192.31
-phiX174	3980	3990	617480.77
-phiX174	3990	4020	632450.00
-phiX174	4020	4030	666130.77
-phiX174	4030	4040	669873.08
-phiX174	4040	4050	636192.31
-phiX174	4050	4070	606253.85
-phiX174	4070	4080	602511.54
-phiX174	4080	4090	621223.08
-phiX174	4090	4100	647419.23
-phiX174	4100	4110	632450.00
-phiX174	4110	4120	636192.31
-phiX174	4120	4130	606253.85
-phiX174	4130	4140	624965.38
-phiX174	4140	4160	636192.31
-phiX174	4160	4170	654903.85
-phiX174	4170	4180	636192.31
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-phiX174	4190	4200	669873.08
-phiX174	4200	4210	707296.15
-phiX174	4210	4230	692326.92
-phiX174	4230	4240	688584.62
-phiX174	4240	4250	726007.69
-phiX174	4250	4260	711038.46
-phiX174	4260	4270	740976.92
-phiX174	4270	4290	744719.23
-phiX174	4290	4310	752203.85
-phiX174	4310	4320	767173.08
-phiX174	4320	4330	770915.38
-phiX174	4330	4340	737234.62
-phiX174	4340	4350	703553.85
-phiX174	4350	4360	711038.46
-phiX174	4360	4380	714780.77
-phiX174	4380	4390	707296.15
-phiX174	4390	4400	673615.38
-phiX174	4400	4410	703553.85
-phiX174	4410	4430	748461.54
-phiX174	4430	4440	759688.46
-phiX174	4440	4450	774657.69
-phiX174	4450	4470	778400.00
-phiX174	4470	4480	759688.46
-phiX174	4480	4490	767173.08
-phiX174	4490	4500	759688.46
-phiX174	4500	4510	729750.00
-phiX174	4510	4520	707296.15
-phiX174	4520	4530	688584.62
-phiX174	4530	4540	692326.92
-phiX174	4540	4550	733492.31
-phiX174	4550	4560	711038.46
-phiX174	4560	4580	703553.85
-phiX174	4580	4590	669873.08
-phiX174	4590	4600	684842.31
-phiX174	4600	4610	707296.15
-phiX174	4610	4620	692326.92
-phiX174	4620	4630	737234.62
-phiX174	4630	4640	733492.31
-phiX174	4640	4650	778400.00
-phiX174	4650	4660	752203.85
-phiX174	4660	4670	748461.54
-phiX174	4670	4680	744719.23
-phiX174	4680	4690	729750.00
-phiX174	4690	4700	770915.38
-phiX174	4700	4710	744719.23
-phiX174	4710	4720	729750.00
-phiX174	4720	4730	733492.31
-phiX174	4730	4740	774657.69
-phiX174	4740	4750	804596.15
-phiX174	4750	4760	800853.85
-phiX174	4760	4770	815823.08
-phiX174	4770	4780	860730.77
-phiX174	4780	4810	868215.38
-phiX174	4810	4830	886926.92
-phiX174	4830	4840	905638.46
-phiX174	4840	4850	931834.62
-phiX174	4850	4860	939319.23
-phiX174	4860	4870	924350.00
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-phiX174	4890	4900	860730.77
-phiX174	4900	4910	845761.54
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-phiX174	4950	4960	789626.92
-phiX174	4960	4970	740976.92
-phiX174	4970	4980	726007.69
-phiX174	4980	4990	699811.54
-phiX174	4990	5000	703553.85
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-phiX174	5010	5030	669873.08
-phiX174	5030	5050	666130.77
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-phiX174	5080	5090	557603.85
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-phiX174	5100	5120	512696.15
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-phiX174	5130	5140	479015.38
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-phiX174	5160	5180	426623.08
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-phiX174	5210	5220	303126.92
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-phiX174	5230	5240	243250.00
-phiX174	5240	5250	209569.23
-phiX174	5250	5260	164661.54
-phiX174	5260	5280	160919.23
-phiX174	5280	5290	130980.77
-phiX174	5290	5300	97300.00
-phiX174	5300	5310	78588.46
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+phiX174	4230	4240	449076.92
+phiX174	4240	4250	471530.77
+phiX174	4250	4260	465917.31
+phiX174	4260	4290	510825.00
+phiX174	4290	4300	522051.92
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+phiX174	4310	4320	555732.69
+phiX174	4320	4330	561346.15
+phiX174	4330	4340	505211.54
+phiX174	4340	4350	477144.23
+phiX174	4350	4370	493984.62
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+phiX174	4380	4390	493984.62
+phiX174	4390	4400	477144.23
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+phiX174	4410	4420	510825.00
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+phiX174	4480	4490	538892.31
+phiX174	4490	4500	550119.23
+phiX174	4500	4510	527665.38
+phiX174	4510	4530	505211.54
+phiX174	4530	4540	516438.46
+phiX174	4540	4550	550119.23
+phiX174	4550	4560	555732.69
+phiX174	4560	4570	533278.85
+phiX174	4570	4580	522051.92
+phiX174	4580	4600	493984.62
+phiX174	4600	4610	505211.54
+phiX174	4610	4620	449076.92
+phiX174	4620	4630	482757.69
+phiX174	4630	4640	471530.77
+phiX174	4640	4650	488371.15
+phiX174	4650	4660	454690.38
+phiX174	4660	4670	465917.31
+phiX174	4670	4690	460303.85
+phiX174	4690	4700	488371.15
+phiX174	4700	4710	482757.69
+phiX174	4710	4720	471530.77
+phiX174	4720	4730	482757.69
+phiX174	4730	4740	510825.00
+phiX174	4740	4750	527665.38
+phiX174	4750	4760	538892.31
+phiX174	4760	4770	561346.15
+phiX174	4770	4790	611867.31
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+phiX174	4850	4860	595026.92
+phiX174	4860	4870	606253.85
+phiX174	4870	4880	600640.38
+phiX174	4880	4900	589413.46
+phiX174	4900	4910	538892.31
+phiX174	4910	4920	533278.85
+phiX174	4920	4930	544505.77
+phiX174	4930	4940	516438.46
+phiX174	4940	4950	482757.69
+phiX174	4950	4960	454690.38
+phiX174	4960	4970	409782.69
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+phiX174	4990	5000	359261.54
+phiX174	5000	5010	392942.31
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+phiX174	5140	5150	370488.46
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+phiX174	5240	5250	162790.38
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+phiX174	5340	5350	22453.85
+phiX174	5350	5386	11226.9
diff -r 627004611e98 -r 9bee2c86eeb1 test-data/bamCoverage_result4.bw
Binary file test-data/bamCoverage_result4.bw has changed
diff -r 627004611e98 -r 9bee2c86eeb1 test-data/correctGCBias_result1.bam
diff -r 627004611e98 -r 9bee2c86eeb1 test-data/heatmapper_result1.png
Binary file test-data/heatmapper_result1.png has changed
diff -r 627004611e98 -r 9bee2c86eeb1 test-data/profiler_result1.png
Binary file test-data/profiler_result1.png has changed
diff -r 627004611e98 -r 9bee2c86eeb1 tool_dependencies.xml
--- a/tool_dependencies.xml	Sun Mar 22 13:02:33 2015 -0400
+++ b/tool_dependencies.xml	Mon May 25 05:16:10 2015 -0400
@@ -1,93 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="numpy" version="1.7.1">
-        <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="scipy" version="0.12.0">
-        <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="pysam" version="0.7.7">
-        <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bx-python" version="0.7.1">
-        <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="ucsc_tools" version="0.1">
-        <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <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" />
     </package>
-    <package name="deepTools" version="1.5.9">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="pysam" version="0.7.7" />
-                    </repository>
-                    <repository changeset_revision="ec30e3f438f4" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="bx-python" version="0.7.1" />
-                    </repository>
-                    <repository changeset_revision="11099cc214d5" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="numpy" version="1.7.1" />
-                    </repository>
-                    <repository changeset_revision="562aa00c2586" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="matplotlib" version="1.2.1" />
-                    </repository>
-                    <repository changeset_revision="d607515b0510" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="scipy" version="0.12.0" />
-                    </repository>
-                    <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="samtools" version="0.1.19" />
-                    </repository>
-                    <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
-                        <package name="ucsc_tools" version="0.1" />
-                    </repository>
-                </action>
-                <action type="make_directory">$INSTALL_DIR/lib/python</action>
-                <action type="shell_command">
-                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
-                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
-                </action>
-
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
-                    <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
-                    <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
-                    <!-- include samtools into PATH -->
-                    <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
-                    <!-- include numpy -->
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
-                    <!-- include matplotlib -->
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[MATPLOTLIB_LIB_PATH]</environment_variable>
-                    <!-- include scipy -->
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
-                    <!-- include bx-python -->
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[BX_PYTHON_PATH]/lib/python</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[BX_PYTHON_PATH]/bin</environment_variable>
-                    <!-- include pysam -->
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYSAM_PATH]/lib/python</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$ENV[PYSAM_PATH]/bin</environment_variable>
-                    <!-- include ucsc tools -->
-                    <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>
-
-                    <!-- disable the config file of deepTools -->
-                    <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
-                </action>
-             </actions>
-         </install>
-         <readme>
-            Installation of deepTools from Fidel Ramirez.
-            https://github.com/fidelram/deepTools
-         </readme>
-     </package>
 </tool_dependency>