Repository 'deeptools_plot_profile'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile

Changeset 1:466df17b2d67 (2016-02-15)
Previous changeset 0:e4ad262c1321 (2016-01-25) Next changeset 2:0b9bc8b4d0c1 (2016-02-18)
Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
modified:
deepTools_macros.xml
plotProfiler.xml
readme.rst
test-data/bamCompare_result2.bw
test-data/bamCoverage_result1.bw
test-data/bamCoverage_result2.bw
test-data/bamCoverage_result4.bw
test-data/bamPEFragmentSize_result1.txt
test-data/bigwigCompare_result1.bw
test-data/computeMatrix2.bed
test-data/computeMatrix2.bw
test-data/correctGCBias_result1.bam
test-data/plotCoverage_result1.png
test-data/plotCoverage_result1.tabular
test-data/sequence.2bit
test-data/test.bw
tool-data/deepTools_seqs.loc.sample
tool_dependencies.xml
added:
deepTools_macros.xml.orig
static/images/GC_bias_simulated_reads_2L.png
static/images/QC_plotCoverage.png
static/images/bamCompare_output.png
static/images/bamCoverage_output.png
static/images/bamPEFragmentSize_output.png
static/images/bigwigCompare_output.png
static/images/computeGCBias_output.png
static/images/computeMatrix_advancedOutput.png
static/images/computeMatrix_output.png
static/images/computeMatrix_overview.png
static/images/computeMatrix_selectRegions.png
static/images/computeMatrix_selectScores.png
static/images/multiBamSummary_output.png
static/images/multiBigwigSummary_output.png
static/images/plotCorrelate_RNAseq.png
static/images/plotCorrelation_output.png
static/images/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png
static/images/plotCoverage_annotated.png
static/images/plotCoverage_output.png
static/images/plotFingerprint_output.png
static/images/plotHeatmap_example.png
static/images/plotHeatmap_example02.png
static/images/plotPCA_annotated.png
static/images/plotProfiler_examples.png
tool_dependencies.xml.orig
removed:
static/images/flowChart_computeMatrixetc.png
b
diff -r e4ad262c1321 -r 466df17b2d67 deepTools_macros.xml
--- a/deepTools_macros.xml Mon Jan 25 20:27:28 2016 -0500
+++ b/deepTools_macros.xml Mon Feb 15 10:34:50 2016 -0500
[
@@ -72,12 +72,12 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.0.1</token>
+    <token name="@WRAPPER_VERSION@">2.1.0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
             <requirement type="binary">@BINARY@</requirement>
-            <requirement type="package" version="2.0.1">deepTools</requirement>
+            <requirement type="package" version="2.1.0">deepTools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -104,6 +104,7 @@
                     <param name="clustering_options" type="select" label="Clustering algorithm">
                         <option value="none">No clustering</option>
                         <option value="kmeans">Kmeans clustering</option>
+                        <option value="hclust">Hierarchical clustering</option>
                     </param>
                     <when value="kmeans">
                         <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
@@ -112,6 +113,15 @@
                             If more specific clustering methods are required it is advisable to save the underlying matrix and
                             run the clustering using other software."/>
                     </when>
+                    <when value="hclust">
+                        <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
+                            help="WARNING: This option causes the tool to run for a very long time! When this option is
+                            set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
+                            This only works for data that is not grouped, otherwise only the first group will be clustered.
+                            Note that you must have used the '--missingDataAsZero' option within computeMatrix!
+                            If more specific clustering methods are required it is advisable to save the underlying matrix and
+                            run the clustering using other software."/>
+                    </when>
                     <when value="none" />
                 </conditional>
             </when>
@@ -126,6 +136,11 @@
                     --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
                 #end if
             #end if
+            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
+                #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
+                    --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
+                #end if
+            #end if
         #end if
     </token>
 
@@ -293,6 +308,12 @@
     </xml>
 
     <xml name="multiple_input_bams">
+        <param argument="--bamfiles" type="data" format="bam" min="1"
+            label="Bam file" multiple="true"
+            help="The BAM file must be sorted."/>
+    </xml>
+
+    <xml name="multiple_input_bams_min2">
         <param argument="--bamfiles" type="data" format="bam" min="2"
             label="Bam file" multiple="true"
             help="The BAM file must be sorted."/>
@@ -310,6 +331,7 @@
             help="Title of the plot, to be printed on top of the generated image." />
     </xml>
 
+
     <token name="@multiple_input_bams@">
 <![CDATA[
         #set files=[]
b
diff -r e4ad262c1321 -r 466df17b2d67 deepTools_macros.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deepTools_macros.xml.orig Mon Feb 15 10:34:50 2016 -0500
b
b'@@ -0,0 +1,639 @@\n+<macros>\n+\n+    <xml name="advancedOpt_scaffold">\n+        <conditional name="advancedOpt">\n+            <param name="showAdvancedOpt" type="select" label="Show advanced options" >\n+                <option value="no" selected="true">no</option>\n+                <option value="yes">yes</option>\n+            </param>\n+            <when value="no" />\n+            <when value="yes">\n+                <yield/>\n+            </when>\n+        </conditional>\n+    </xml>\n+\n+    <token name="@ADVANCED_OPTS_READ_PROCESSING@">\n+        #if $advancedOpt.doExtendCustom.doExtend == \'custom\':\n+            --extendReads $advancedOpt.doExtendCustom.extendReadsValue\n+        #else if $advancedOpt.doExtendCustom.doExtend == \'yes\':\n+            --extendReads\n+        #end if\n+        $advancedOpt.ignoreDuplicates\n+        $advancedOpt.centerReads\n+        #if $advancedOpt.minMappingQuality:\n+            --minMappingQuality \'$advancedOpt.minMappingQuality\'\n+        #end if\n+        #if $advancedOpt.samFlagInclude:\n+            --samFlagInclude $advancedOpt.samFlagInclude\n+        #end if\n+        #if $advancedOpt.samFlagExclude:\n+            --samFlagExclude $advancedOpt.samFlagExclude\n+        #end if\n+    </token>\n+\n+    <xml name="heatmap_options">\n+        <expand macro="zMin_zMax" />\n+        <expand macro="colorMap" />\n+        <expand macro="plotTitle" />\n+        <expand macro="plotNumbers" />\n+    </xml>\n+\n+    <token name="@HEATMAP_OPTIONS@">\n+        #if str($plotting_type.zMin) != "":\n+            --zMin $plotting_type.zMin\n+        #end if\n+        #if str($plotting_type.zMax) != "":\n+            --zMax $plotting_type.zMax\n+        #end if\n+        --colorMap \'$plotting_type.colorMap\'\n+        $plotting_type.plotNumbers\n+        --plotTitle \'$plotting_type.plotTitle\'\n+    </token>\n+\n+\n+    <xml name="includeZeros">\n+        <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""\n+            label="Include zeros"\n+            help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />\n+    </xml>\n+\n+    <xml name="zMin_zMax">\n+        <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"\n+            help="If not specified the value is set automatically."/>\n+        <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"\n+            help="If not specified the value is set automatically."/>\n+    </xml>\n+\n+    <xml name="region_limit_operation">\n+        <param argument="--region" type="text" value=""\n+            label="Region of the genome to limit the operation to"\n+            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />\n+    </xml>\n+\n+    <token name="@THREADS@">--numberOfProcessors "\\${GALAXY_SLOTS:-4}"</token>\n+<<<<<<< HEAD\n+    <token name="@WRAPPER_VERSION@">2.0.1.0</token>\n+=======\n+    <token name="@WRAPPER_VERSION@">2.1.0</token>\n+>>>>>>> d56067f86089e75354a2fad266002db3730766d9\n+    <xml name="requirements">\n+        <requirements>\n+            <requirement type="package" version="2.7.10">python</requirement>\n+            <requirement type="binary">@BINARY@</requirement>\n+<<<<<<< HEAD\n+            <requirement type="package" version="2.0.1">deepTools</requirement>\n+=======\n+            <requirement type="package" version="2.1.0">deepTools</requirement>\n+>>>>>>> d56067f86089e75354a2fad266002db3730766d9\n+            <yield />\n+        </requirements>\n+        <expand macro="stdio" />\n+        <version_command>@BINARY@ --version</version_command>\n+    </xml>\n+\n+    <xml name="smoothLength">\n+        <param argument="--smoothLength" type="integer" value="" optional="True" min="1"\n+            label="Smooth values using the following length (in bases)"\n+            help '..b'k2 reversed</option>\n+            <option value="Reds_r">Reds reversed</option>\n+            <option value="Oranges_r">Oranges reversed</option>\n+            <option value="Greens_r">Greens reversed</option>\n+            <option value="Blues_r">Blues reversed</option>\n+            <option value="Greys_r">Greys reversed</option>\n+            <option value="Purples_r">Purples reversed</option>\n+            <option value="Paired_r">Paired reversed</option>\n+            <option value="Pastel1_r">Pastel1 reversed</option>\n+            <option value="Pastel2_r">Pastel2 reversed</option>\n+            <option value="spring_r">spring reversed</option>\n+            <option value="summer_r">summer reversed</option>\n+            <option value="autumn_r">autumn reversed</option>\n+            <option value="winter_r">winter reversed</option>\n+            <option value="hot_r">hot reversed</option>\n+            <option value="coolwarm_r">coolwarm reversed</option>\n+            <option value="cool_r">cool reversed</option>\n+            <option value="seismic_r">seismic reversed</option>\n+            <option value="terrain_r">terrain reversed</option>\n+            <option value="ocean_r">ocean reversed</option>\n+            <option value="rainbow_r">rainbow reversed</option>\n+            <option value="bone_r">bone reversed</option>\n+            <option value="flag_r">flag reversed</option>\n+            <option value="prism_r">prism reversed</option>\n+            <option value="cubehelix_r">cubehelix reversed</option>\n+            <option value="binary_r">binary reversed</option>\n+            <option value="pink_r">pink reversed</option>\n+            <option value="gray_r">gray reversed</option>\n+            <option value="copper_r">copper reversed</option>\n+            <option value="BrBG_r">BrBG reversed</option>\n+            <option value="BuGn_r">BuGn reversed</option>\n+            <option value="BuPu_r">BuPu reversed</option>\n+            <option value="GnBu_r">GnBu reversed</option>\n+            <option value="OrRd_r">OrRd reversed</option>\n+            <option value="PiYG_r">PiYG reversed</option>\n+            <option value="PRGn_r">PRGn reversed</option>\n+            <option value="PuOr_r">PuOr reversed</option>\n+            <option value="PuRd_r">PuRd reversed</option>\n+            <option value="PuBu_r">PuBu reversed</option>\n+            <option value="RdBu_r">RdBu reversed</option>\n+            <option value="RdGy_r">RdGy reversed</option>\n+            <option value="RdPu_r">RdPu reversed</option>\n+            <option value="YlGn_r">YlGn reversed</option>\n+            <option value="PuBuGn_r">PuBuGn reversed</option>\n+            <option value="RdYlBu_r">RdYlBu reversed</option>\n+            <option value="RdYlGn_r">RdYlGn reversed</option>\n+            <option value="YlGnBu_r">YlGnBu reversed</option>\n+            <option value="YlOrBr_r">YlOrBr reversed</option>\n+            <option value="YlOrRd_r">YlOrRd reversed</option>\n+            <option value="gist_gray_r">gist_gray reversed</option>\n+            <option value="gist_stern_r">gist_stern reversed</option>\n+            <option value="gist_earth_r">gist_earth reversed</option>\n+            <option value="gist_yarg_r">gist_yarg reversed</option>\n+            <option value="gist_ncar_r">gist_ncar reversed</option>\n+            <option value="gist_rainbow_r">gist_rainbow reversed</option>\n+            <option value="gist_heat_r">gist_heat reversed</option>\n+            <option value="gnuplot_r">gnuplot reversed</option>\n+            <option value="gnuplot2_r">gnuplot2 reversed</option>\n+            <option value="CMRmap_r">CMRmap reversed</option>\n+            <option value="bwr_r">bwr reversed</option>\n+            <option value="hsv_r">hsv reversed</option>\n+            <option value="brg_r">brg reversed</option>\n+            <option value="jet_r">jet reversed</option>\n+            <option value="afmhot_r">afmhot reversed</option>\n+        </param>\n+\n+    </xml>\n+\n+</macros>\n'
b
diff -r e4ad262c1321 -r 466df17b2d67 plotProfiler.xml
--- a/plotProfiler.xml Mon Jan 25 20:27:28 2016 -0500
+++ b/plotProfiler.xml Mon Feb 15 10:34:50 2016 -0500
[
@@ -1,6 +1,6 @@
 <tool id="deeptools_plot_profile" name="plotProfile" version="@WRAPPER_VERSION@.0">
     <description>
-        creates a profile plot for a score associated to genomic regions
+        creates a profile plot for score distributions across genomic regions
     </description>
     <macros>
         <token name="@BINARY@">plotProfile</token>
@@ -35,7 +35,13 @@
                 --plotHeight $advancedOpt.plotHeight
                 --plotWidth $advancedOpt.plotWidth
                 --plotType $advancedOpt.plotType
-                --regionsLabel '$advancedOpt.regionsLabel'
+                #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
+                    --samplesLabel $advancedOpt.samplesLabel
+                #end if
+
+                #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
+                    --regionsLabel $advancedOpt.regionsLabel
+                #end if
 
                 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle).strip() != "":
                     --plotTitle '$advancedOpt.plotTitle'
@@ -102,9 +108,9 @@
                     label="Plot height"
                     help="Height in cm. The default for the plot height is 5 centimeters. The minimum value is 3 cm." />
 
-                <param argument="--plotWidth" type="integer" value="8" min="1"
+                <param argument="--plotWidth" type="integer" value="11" min="1"
                     label="Plot width"
-                    help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
+                    help="Width in cm. The default value is 11 centimeters. The minimum value is 1 cm." />
 
                 <param argument="--plotType" type="select" label="Plot type"
                     help="The &quot;lines&quot; option will
@@ -120,10 +126,20 @@
                     <option value="se">add standard error</option>
                     <option value="overlapped_lines">overlapped lines</option>
                 </param>
-                <param argument="--regionsLabel" type="text" value="coverage" size="30"
+                <param argument="--samplesLabel" type="text" size="30"
+                    label="Labels for the samples (each bigwig) plotted"
+                    help="The default is to use the file name of the sample. The sample labels should be separated by
+                    spaces and quoted if a label itself contains a space, e.g., label-1 &quot;label 2&quot;">
+                    <sanitizer>
+                        <valid initial="string.printable">
+                        </valid>
+                    </sanitizer>
+                </param>
+                <param argument="--regionsLabel" type="text" 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 commas is required. For example, &quot;label1, label2&quot;."/>
+                    help="If more than one region is being plotted a list of labels separated by space is required.
+                          If a label itself contains a space, then quotes are needed.
+                          For example, label_1, &quot;label 2&quot;" />
 
                 <expand macro="plotTitle" />
                 <param argument="--colors" type="text" value="" size="40"
@@ -135,9 +151,8 @@
                 </param>
 
                 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
-                    label="Do one plot per group"
-                    help="When clustering is applied to the data or multiple BED files were used,
-                    plot the groups next to each other. The default is to plot the samples next to each other." />
+                    label="Make one plot per group of regions"
+                    help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions. " />
 
 
                 <param argument="--yMin" type="float" value="" size="3" optional="true"
@@ -169,21 +184,37 @@
     <help>
 <![CDATA[
 
-**What it does**
+What it does
+-------------
 
 This tool plots the average enrichments over all genomic
-regions supplied to computeMarix. It requires that computeMatrix was successfully run.
-It is a very useful complement to the heatmapper, especially in cases where you want to
-compare the scores for many different groups. Like heatmapper, profiler does not change the
-values that were compute by computeMatrix, but you can modify the color and other display properties of the plots.
+regions supplied to ``computeMarix``. It requires that ``computeMatrix`` was successfully run.
+It is a very useful complement to ``plotHeatmap``, especially in cases where you want to
+compare the scores for many different groups. Like ``plotHeatmap``, ``plotProfile`` does not change the
+values that were computed by ``computeMatrix``, but you can modify the color and other display properties of the plots.
 
+Output
+-------------
+
+.. image:: $PATH_TO_IMAGES/plotProfiler_examples.png
+   :width: 600
+   :height: 858
+
+=======
 
-.. image:: $PATH_TO_IMAGES/visual_profiler_DmelPolII.png
-   :alt: Meta-gene profile of Rna Polymerase II
+In addition to the image, ``plotProfile`` can also generate the values underlying the profile.
+
+See the following table for the **optional output** options:
 
-
-You can find more details on the profiler doc page: https://deeptools.readthedocs.org/en/master/content/tools/plotProfile.html
-
++-----------------------------------+--------------------+-----------------+-----------------+
+|  **optional output type**         |  **computeMatrix** | **plotHeatmap** | **plotProfile** |
++-----------------------------------+--------------------+-----------------+-----------------+
+| values underlying the heatmap     |  yes               | yes             | no              |
++-----------------------------------+--------------------+-----------------+-----------------+
+| values underlying the profile     | no                 | no              | yes             |
++-----------------------------------+--------------------+-----------------+-----------------+
+| sorted and/or filtered regions    | yes                | yes             | yes             |
++-----------------------------------+--------------------+-----------------+-----------------+
 
 -----
 
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/GC_bias_simulated_reads_2L.png
b
Binary file static/images/GC_bias_simulated_reads_2L.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/QC_plotCoverage.png
b
Binary file static/images/QC_plotCoverage.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/bamCompare_output.png
b
Binary file static/images/bamCompare_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/bamCoverage_output.png
b
Binary file static/images/bamCoverage_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/bamPEFragmentSize_output.png
b
Binary file static/images/bamPEFragmentSize_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/bigwigCompare_output.png
b
Binary file static/images/bigwigCompare_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/computeGCBias_output.png
b
Binary file static/images/computeGCBias_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/computeMatrix_advancedOutput.png
b
Binary file static/images/computeMatrix_advancedOutput.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/computeMatrix_output.png
b
Binary file static/images/computeMatrix_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/computeMatrix_overview.png
b
Binary file static/images/computeMatrix_overview.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/computeMatrix_selectRegions.png
b
Binary file static/images/computeMatrix_selectRegions.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/computeMatrix_selectScores.png
b
Binary file static/images/computeMatrix_selectScores.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/flowChart_computeMatrixetc.png
b
Binary file static/images/flowChart_computeMatrixetc.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/multiBamSummary_output.png
b
Binary file static/images/multiBamSummary_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/multiBigwigSummary_output.png
b
Binary file static/images/multiBigwigSummary_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotCorrelate_RNAseq.png
b
Binary file static/images/plotCorrelate_RNAseq.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotCorrelation_output.png
b
Binary file static/images/plotCorrelation_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png
b
Binary file static/images/plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotCoverage_annotated.png
b
Binary file static/images/plotCoverage_annotated.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotCoverage_output.png
b
Binary file static/images/plotCoverage_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotFingerprint_output.png
b
Binary file static/images/plotFingerprint_output.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotHeatmap_example.png
b
Binary file static/images/plotHeatmap_example.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotHeatmap_example02.png
b
Binary file static/images/plotHeatmap_example02.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotPCA_annotated.png
b
Binary file static/images/plotPCA_annotated.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 static/images/plotProfiler_examples.png
b
Binary file static/images/plotProfiler_examples.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 test-data/bamCompare_result2.bw
b
Binary file test-data/bamCompare_result2.bw has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 test-data/bamCoverage_result1.bw
b
Binary file test-data/bamCoverage_result1.bw has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 test-data/bamCoverage_result2.bw
b
Binary file test-data/bamCoverage_result2.bw has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 test-data/bamCoverage_result4.bw
b
Binary file test-data/bamCoverage_result4.bw has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt Mon Jan 25 20:27:28 2016 -0500
+++ b/test-data/bamPEFragmentSize_result1.txt Mon Feb 15 10:34:50 2016 -0500
b
@@ -2,19 +2,19 @@
 
 
 Fragment lengths:
-Min.: 241
+Min.: 241.0
 1st Qu.: 241.5
 Mean: 244.666666667
 Median: 242.0
 3rd Qu.: 246.5
-Max.: 251
+Max.: 251.0
 Std: 4.49691252108
 
 Read lengths:
-Min.: 251
+Min.: 251.0
 1st Qu.: 251.0
 Mean: 251.0
 Median: 251.0
 3rd Qu.: 251.0
-Max.: 251
+Max.: 251.0
 Std: 0.0
b
diff -r e4ad262c1321 -r 466df17b2d67 test-data/bigwigCompare_result1.bw
b
Binary file test-data/bigwigCompare_result1.bw has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 test-data/correctGCBias_result1.bam
b
Binary file test-data/correctGCBias_result1.bam has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 test-data/plotCoverage_result1.png
b
Binary file test-data/plotCoverage_result1.png has changed
b
diff -r e4ad262c1321 -r 466df17b2d67 test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular Mon Jan 25 20:27:28 2016 -0500
+++ b/test-data/plotCoverage_result1.tabular Mon Feb 15 10:34:50 2016 -0500
b
b"@@ -1,16570 +1,16570 @@\n-'bowtie2-test1.bam'\t'bowtie2-test1.bam'\n-23\t23\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-35\t35\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-33\t33\n-27\t27\n-25\t25\n-24\t24\n-21\t21\n-20\t20\n-19\t19\n-19\t19\n-19\t19\n-17\t17\n-17\t17\n-15\t15\n-15\t15\n-15\t15\n-10\t10\n-7\t7\n-7\t7\n-7\t7\n-7\t7\n-6\t6\n-5\t5\n-5\t5\n-5\t5\n-3\t3\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n-0\t0\n"..b'\t16415\t16416\t0.0\t0.0\n+chrM\t16416\t16417\t0.0\t0.0\n+chrM\t16417\t16418\t0.0\t0.0\n+chrM\t16418\t16419\t0.0\t0.0\n+chrM\t16419\t16420\t0.0\t0.0\n+chrM\t16420\t16421\t0.0\t0.0\n+chrM\t16421\t16422\t0.0\t0.0\n+chrM\t16422\t16423\t0.0\t0.0\n+chrM\t16423\t16424\t0.0\t0.0\n+chrM\t16424\t16425\t0.0\t0.0\n+chrM\t16425\t16426\t0.0\t0.0\n+chrM\t16426\t16427\t0.0\t0.0\n+chrM\t16427\t16428\t0.0\t0.0\n+chrM\t16428\t16429\t0.0\t0.0\n+chrM\t16429\t16430\t0.0\t0.0\n+chrM\t16430\t16431\t0.0\t0.0\n+chrM\t16431\t16432\t0.0\t0.0\n+chrM\t16432\t16433\t0.0\t0.0\n+chrM\t16433\t16434\t0.0\t0.0\n+chrM\t16434\t16435\t0.0\t0.0\n+chrM\t16435\t16436\t0.0\t0.0\n+chrM\t16436\t16437\t0.0\t0.0\n+chrM\t16437\t16438\t0.0\t0.0\n+chrM\t16438\t16439\t0.0\t0.0\n+chrM\t16439\t16440\t0.0\t0.0\n+chrM\t16440\t16441\t0.0\t0.0\n+chrM\t16441\t16442\t0.0\t0.0\n+chrM\t16442\t16443\t0.0\t0.0\n+chrM\t16443\t16444\t0.0\t0.0\n+chrM\t16444\t16445\t0.0\t0.0\n+chrM\t16445\t16446\t0.0\t0.0\n+chrM\t16446\t16447\t0.0\t0.0\n+chrM\t16447\t16448\t0.0\t0.0\n+chrM\t16448\t16449\t0.0\t0.0\n+chrM\t16449\t16450\t0.0\t0.0\n+chrM\t16450\t16451\t0.0\t0.0\n+chrM\t16451\t16452\t0.0\t0.0\n+chrM\t16452\t16453\t0.0\t0.0\n+chrM\t16453\t16454\t0.0\t0.0\n+chrM\t16454\t16455\t0.0\t0.0\n+chrM\t16455\t16456\t0.0\t0.0\n+chrM\t16456\t16457\t0.0\t0.0\n+chrM\t16457\t16458\t0.0\t0.0\n+chrM\t16458\t16459\t0.0\t0.0\n+chrM\t16459\t16460\t0.0\t0.0\n+chrM\t16460\t16461\t0.0\t0.0\n+chrM\t16461\t16462\t0.0\t0.0\n+chrM\t16462\t16463\t0.0\t0.0\n+chrM\t16463\t16464\t0.0\t0.0\n+chrM\t16464\t16465\t0.0\t0.0\n+chrM\t16465\t16466\t0.0\t0.0\n+chrM\t16466\t16467\t0.0\t0.0\n+chrM\t16467\t16468\t0.0\t0.0\n+chrM\t16468\t16469\t0.0\t0.0\n+chrM\t16469\t16470\t0.0\t0.0\n+chrM\t16470\t16471\t0.0\t0.0\n+chrM\t16471\t16472\t0.0\t0.0\n+chrM\t16472\t16473\t0.0\t0.0\n+chrM\t16473\t16474\t0.0\t0.0\n+chrM\t16474\t16475\t0.0\t0.0\n+chrM\t16475\t16476\t0.0\t0.0\n+chrM\t16476\t16477\t0.0\t0.0\n+chrM\t16477\t16478\t0.0\t0.0\n+chrM\t16478\t16479\t0.0\t0.0\n+chrM\t16479\t16480\t0.0\t0.0\n+chrM\t16480\t16481\t0.0\t0.0\n+chrM\t16481\t16482\t0.0\t0.0\n+chrM\t16482\t16483\t0.0\t0.0\n+chrM\t16483\t16484\t0.0\t0.0\n+chrM\t16484\t16485\t0.0\t0.0\n+chrM\t16485\t16486\t0.0\t0.0\n+chrM\t16486\t16487\t0.0\t0.0\n+chrM\t16487\t16488\t0.0\t0.0\n+chrM\t16488\t16489\t0.0\t0.0\n+chrM\t16489\t16490\t0.0\t0.0\n+chrM\t16490\t16491\t0.0\t0.0\n+chrM\t16491\t16492\t0.0\t0.0\n+chrM\t16492\t16493\t0.0\t0.0\n+chrM\t16493\t16494\t0.0\t0.0\n+chrM\t16494\t16495\t0.0\t0.0\n+chrM\t16495\t16496\t0.0\t0.0\n+chrM\t16496\t16497\t0.0\t0.0\n+chrM\t16497\t16498\t0.0\t0.0\n+chrM\t16498\t16499\t0.0\t0.0\n+chrM\t16499\t16500\t0.0\t0.0\n+chrM\t16500\t16501\t0.0\t0.0\n+chrM\t16501\t16502\t0.0\t0.0\n+chrM\t16502\t16503\t0.0\t0.0\n+chrM\t16503\t16504\t0.0\t0.0\n+chrM\t16504\t16505\t0.0\t0.0\n+chrM\t16505\t16506\t0.0\t0.0\n+chrM\t16506\t16507\t0.0\t0.0\n+chrM\t16507\t16508\t0.0\t0.0\n+chrM\t16508\t16509\t0.0\t0.0\n+chrM\t16509\t16510\t0.0\t0.0\n+chrM\t16510\t16511\t0.0\t0.0\n+chrM\t16511\t16512\t0.0\t0.0\n+chrM\t16512\t16513\t0.0\t0.0\n+chrM\t16513\t16514\t0.0\t0.0\n+chrM\t16514\t16515\t0.0\t0.0\n+chrM\t16515\t16516\t0.0\t0.0\n+chrM\t16516\t16517\t0.0\t0.0\n+chrM\t16517\t16518\t0.0\t0.0\n+chrM\t16518\t16519\t0.0\t0.0\n+chrM\t16519\t16520\t0.0\t0.0\n+chrM\t16520\t16521\t0.0\t0.0\n+chrM\t16521\t16522\t0.0\t0.0\n+chrM\t16522\t16523\t0.0\t0.0\n+chrM\t16523\t16524\t0.0\t0.0\n+chrM\t16524\t16525\t0.0\t0.0\n+chrM\t16525\t16526\t0.0\t0.0\n+chrM\t16526\t16527\t0.0\t0.0\n+chrM\t16527\t16528\t0.0\t0.0\n+chrM\t16528\t16529\t0.0\t0.0\n+chrM\t16529\t16530\t0.0\t0.0\n+chrM\t16530\t16531\t0.0\t0.0\n+chrM\t16531\t16532\t0.0\t0.0\n+chrM\t16532\t16533\t0.0\t0.0\n+chrM\t16533\t16534\t0.0\t0.0\n+chrM\t16534\t16535\t0.0\t0.0\n+chrM\t16535\t16536\t0.0\t0.0\n+chrM\t16536\t16537\t0.0\t0.0\n+chrM\t16537\t16538\t0.0\t0.0\n+chrM\t16538\t16539\t0.0\t0.0\n+chrM\t16539\t16540\t0.0\t0.0\n+chrM\t16540\t16541\t0.0\t0.0\n+chrM\t16541\t16542\t0.0\t0.0\n+chrM\t16542\t16543\t0.0\t0.0\n+chrM\t16543\t16544\t0.0\t0.0\n+chrM\t16544\t16545\t0.0\t0.0\n+chrM\t16545\t16546\t0.0\t0.0\n+chrM\t16546\t16547\t0.0\t0.0\n+chrM\t16547\t16548\t0.0\t0.0\n+chrM\t16548\t16549\t0.0\t0.0\n+chrM\t16549\t16550\t0.0\t0.0\n+chrM\t16550\t16551\t0.0\t0.0\n+chrM\t16551\t16552\t0.0\t0.0\n+chrM\t16552\t16553\t0.0\t0.0\n+chrM\t16553\t16554\t0.0\t0.0\n+chrM\t16554\t16555\t0.0\t0.0\n+chrM\t16555\t16556\t0.0\t0.0\n+chrM\t16556\t16557\t0.0\t0.0\n+chrM\t16557\t16558\t0.0\t0.0\n+chrM\t16558\t16559\t0.0\t0.0\n+chrM\t16559\t16560\t0.0\t0.0\n+chrM\t16560\t16561\t0.0\t0.0\n+chrM\t16561\t16562\t0.0\t0.0\n+chrM\t16562\t16563\t0.0\t0.0\n+chrM\t16563\t16564\t0.0\t0.0\n+chrM\t16564\t16565\t0.0\t0.0\n+chrM\t16565\t16566\t0.0\t0.0\n+chrM\t16566\t16567\t0.0\t0.0\n+chrM\t16567\t16568\t0.0\t0.0\n+chrM\t16568\t16569\t0.0\t0.0\n'
b
diff -r e4ad262c1321 -r 466df17b2d67 tool_dependencies.xml
--- a/tool_dependencies.xml Mon Jan 25 20:27:28 2016 -0500
+++ b/tool_dependencies.xml Mon Feb 15 10:34:50 2016 -0500
b
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="python" version="2.7.10">
-        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="deepTools" version="2.0.1">
-        <repository changeset_revision="1fb61fa32733" name="package_python_2_7_deeptools_2_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="deepTools" version="2.1.0">
+        <repository changeset_revision="2c54c7c38299" name="package_python_2_7_deeptools_2_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
b
diff -r e4ad262c1321 -r 466df17b2d67 tool_dependencies.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml.orig Mon Feb 15 10:34:50 2016 -0500
[
@@ -0,0 +1,76 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool_dependency>
+    <package name="numpy" version="1.9">
+        <repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="pybigwig" version="0.2.4">
+        <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc" prior_installation_required="True"/>
+    </package>
+    <package name="matplotlib" version="1.4">
+        <repository name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="scipy" version="0.14">
+        <repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" />
+    </package>
+<<<<<<< HEAD
+    <package name="deepTools" version="2.0.1">
+        <repository name="package_python_2_7_deeptools_2_0_1" owner="iuc"/>
+=======
+    <package name="pysam" version="0.8.3">
+        <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="bx-python" version="0.7.2">
+        <repository name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" />
+    </package>
+    <package name="python" version="2.7.10">
+        <repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" />
+>>>>>>> d56067f86089e75354a2fad266002db3730766d9
+    </package>
+    <package name="deepTools" version="2.1.0">
+        <install version="1.0">
+            <actions>
+                <action type="setup_python_environment">
+                    <repository name="package_python_2_7_10" owner="iuc">
+                        <package name="python" version="2.7.10" />
+                    </repository>
+                    <repository name="package_python_2_7_pysam_0_8_3" owner="iuc">
+                        <package name="pysam" version="0.8.3" />
+                    </repository>
+                    <repository name="package_python_2_7_numpy_1_9" owner="iuc">
+                        <package name="numpy" version="1.9" />
+                    </repository>
+                    <repository name="package_python_2_7_matplotlib_1_4" owner="iuc">
+                        <package name="matplotlib" version="1.4" />
+                    </repository>
+                    <repository name="package_python_2_7_scipy_0_14" owner="iuc">
+                        <package name="scipy" version="0.14" />
+                    </repository>
+                    <repository name="package_python_2_7_bx_python_0_7" owner="iuc">
+                        <package name="bx-python" version="0.7.2" />
+                    </repository>
+                    <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc">
+                        <package name="pybigwig" version="0.2.4" />
+                    </repository>
+                    <package sha256sum="3bf835afde02cd5247198db3e01f690899e1fdb86e1821a83ac940d807baa857">https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz</package>
+                </action>
+
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="DEEPTOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="DEEPTOOLS_PYTHONPATH" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="DEEPTOOLS_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
+                    <!-- libpng lib path -->
+                    <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
+                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
+                    <!-- disable the config file of deepTools -->
+                    <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable>
+                </action>
+             </actions>
+         </install>
+         <readme>
+            Installation of deepTools from Fidel Ramirez.
+            https://github.com/fidelram/deepTools
+         </readme>
+     </package>
+</tool_dependency>