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

Changeset 1:edc6597ff21e (2016-02-15)
Previous changeset 0:268ab1ca4091 (2016-01-25) Next changeset 2:e169677bacd8 (2016-02-18)
Commit message:
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
modified:
deepTools_macros.xml
plotCoverage.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 268ab1ca4091 -r edc6597ff21e deepTools_macros.xml
--- a/deepTools_macros.xml Mon Jan 25 20:21:48 2016 -0500
+++ b/deepTools_macros.xml Mon Feb 15 10:30:33 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 268ab1ca4091 -r edc6597ff21e deepTools_macros.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/deepTools_macros.xml.orig Mon Feb 15 10:30:33 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 268ab1ca4091 -r edc6597ff21e plotCoverage.xml
--- a/plotCoverage.xml Mon Jan 25 20:21:48 2016 -0500
+++ b/plotCoverage.xml Mon Feb 15 10:30:33 2016 -0500
[
@@ -1,5 +1,5 @@
 <tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
-    <description>plots a histogram of coverage on genomic regions </description>
+    <description>assesses the sequencing depth of BAM files </description>
     <macros>
         <token name="@BINARY@">plotCoverage</token>
         <import>deepTools_macros.xml</import>
@@ -82,16 +82,37 @@
             <param name="plotTitle" value="Test Title from Galaxy" />
             <param name="outRawCounts" value="True" />
             <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
-            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="100" />
+            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="500" />
         </test>
     </tests>
     <help>
 <![CDATA[
-**What it does**
+What it does
+-------------
+
+This tool is useful to **assess the sequencing depth** of a given sample.
+It samples 1 million bp, counts the number of overlapping reads and reports
+a coverage histogram that tells you how many bases are covered how many times.
+
+**Note:** Multiple BAM files are accepted but all should correspond to the same genome assembly.
+
+Output
+---------
 
-This tools samples 1 million positions in the genome to build
-a coverage histogram. Multiple bam files are accepted but all should
-correspond to the same genome assembly.
+The default output is a **panel of two plots** (see below for an example): One is a density plot visualizing the frequencies of read coverages, the other one lets you estimate what fraction of the genome has a depth of sequencing of, for example, 2 overlapping reads or more.
+
+The optional output is a table where each row represents the number of reads overlapping with a sampled bp.
+
+.. image:: $PATH_TO_IMAGES/plotCoverage_output.png
+   :width: 600
+   :height: 345
+
+Example plot
+-----------------
+
+.. image:: $PATH_TO_IMAGES/plotCoverage_annotated.png
+   :width: 600
+   :height: 291
 
 
 @REFERENCES@
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diff -r 268ab1ca4091 -r edc6597ff21e test-data/bamCoverage_result1.bw
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diff -r 268ab1ca4091 -r edc6597ff21e test-data/bamCoverage_result4.bw
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diff -r 268ab1ca4091 -r edc6597ff21e test-data/bamPEFragmentSize_result1.txt
--- a/test-data/bamPEFragmentSize_result1.txt Mon Jan 25 20:21:48 2016 -0500
+++ b/test-data/bamPEFragmentSize_result1.txt Mon Feb 15 10:30:33 2016 -0500
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@@ -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
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diff -r 268ab1ca4091 -r edc6597ff21e test-data/plotCoverage_result1.png
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diff -r 268ab1ca4091 -r edc6597ff21e test-data/plotCoverage_result1.tabular
--- a/test-data/plotCoverage_result1.tabular Mon Jan 25 20:21:48 2016 -0500
+++ b/test-data/plotCoverage_result1.tabular Mon Feb 15 10:30:33 2016 -0500
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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 268ab1ca4091 -r edc6597ff21e tool_dependencies.xml
--- a/tool_dependencies.xml Mon Jan 25 20:21:48 2016 -0500
+++ b/tool_dependencies.xml Mon Feb 15 10:30:33 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 268ab1ca4091 -r edc6597ff21e tool_dependencies.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml.orig Mon Feb 15 10:30:33 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>