# HG changeset patch
# User bgruening
# Date 1490966818 14400
# Node ID 94b05ea802031e1836351f35f083f649b46779ac
# Parent  4ae546bddd00602a6cba81982d438308e13e6315
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289

diff -r 4ae546bddd00 -r 94b05ea80203 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Jan 24 04:56:34 2017 -0500
+++ b/deepTools_macros.xml	Fri Mar 31 09:26:58 2017 -0400
@@ -1,5 +1,17 @@
 <macros>
 
+    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
+    <token name="@WRAPPER_VERSION@">2.5.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="2.7.10">python</requirement>
+            <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
+            <yield />
+        </requirements>
+        <expand macro="stdio" />
+        <version_command>@BINARY@ --version</version_command>
+    </xml>
+
     <xml name="advancedOpt_scaffold">
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -97,18 +109,6 @@
         </param>
     </xml>
 
-    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.4.2</token>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="2.7.10">python</requirement>
-            <requirement type="package" version="2.4.2">deeptools</requirement>
-            <yield />
-        </requirements>
-        <expand macro="stdio" />
-        <version_command>@BINARY@ --version</version_command>
-    </xml>
-
     <xml name="smoothLength">
         <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
             label="Smooth values using the following length (in bases)"
@@ -181,10 +181,10 @@
     <xml name="fragLength">
         <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
             label="Minimum fragment length for inclusion."
-            help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
+            help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
         <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
             label="Maximum fragment length for inclusion."
-            help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
+            help="A value of 0 (the default) is equivalent to no maximum." />
     </xml>
 
     <xml name="read_processing_options">
@@ -324,9 +324,7 @@
 
     <xml name="scaleFactor">
         <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
-            help="When used in combination with --normalizeTo1x or
-                --normalizeUsingRPKM, the computed scaling factor will
-                be multiplied by the given scale factor." />
+            help="The computed scaling factor will be multiplied by this (default 1)." />
     </xml>
 
     <xml name="scaleFactors">
@@ -441,19 +439,22 @@
 <![CDATA[
         #set files=[]
         #set labels=[]
+        #import re
         #if $multibam_conditional.orderMatters == "No":
             #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
+                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
                 ln -s "${bamfile}" "./${counter}.bam" &&
                 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
                 #silent $files.append('%s.bam' % $counter)
-                #silent $labels.append("'%s'" % ($bamfile.display_name))
+                #silent $labels.append("'%s'" % identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
+                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                 ln -s "${f.bamfiles}" "./${counter}.bam" &&
                 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
                 #silent $files.append('%s.bam' % $counter)
-                #silent $labels.append("'%s'" % ($f.bamfiles.display_name))
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
 ]]>
@@ -463,17 +464,20 @@
 <![CDATA[
         #set files=[]
         #set labels=[]
+        #import re
         #if $multibigwig_conditional.orderMatters == "No":
             #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
+            #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                 ln -s "${bigwig}" "${counter}.bw" &&
                 #silent $files.append('%s.bw' % $counter)
-                #silent $labels.append("'%s'" % ($bigwig.display_name))
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #else:
             #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
+                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
                 ln -s "${f.bigwigfiles}" "${counter}.bw" &&
                 #silent $files.append('%s.bw' % $counter)
-                #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name))
+                #silent $labels.append("'%s'" % $identifier)
             #end for
         #end if
 ]]>
diff -r 4ae546bddd00 -r 94b05ea80203 plotCoverage.xml
--- a/plotCoverage.xml	Tue Jan 24 04:56:34 2017 -0500
+++ b/plotCoverage.xml	Fri Mar 31 09:26:58 2017 -0400
@@ -1,124 +1,124 @@
-<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
-    <description>assesses the sequencing depth of BAM files </description>
-    <macros>
-        <token name="@BINARY@">plotCoverage</token>
-        <import>deepTools_macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <command>
-<![CDATA[
-        #set files=[]
-        #set labels=[]
-
-        @multiple_input_bams@
-
-        @BINARY@
-
-            @THREADS@
-
-            --plotFile '$outFileName'
-            --bamfiles #echo " ".join($files)#
-            --labels #echo " ".join($labels)#
-            --plotFileFormat "$outFileFormat"
-
-            #if $outRawCounts:
-                --outRawCounts '$outFileRawCounts'
-            #end if
-
-            #if $advancedOpt.showAdvancedOpt == "yes":
-                --numberOfSamples '$advancedOpt.numberOfSamples'
-                $advancedOpt.skipZeros
-
-                #if str($advancedOpt.region).strip() != '':
-                    --region '$advancedOpt.region'
-                #end if
-                --numberOfSamples $advancedOpt.numberOfSamples
-
-                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
-                    --plotTitle '$advancedOpt.plotTitle'
-                #end if
-                @ADVANCED_OPTS_READ_PROCESSING@
-                @blacklist@
-            #end if
-
-]]>
-    </command>
-    <inputs>
-
-        <expand macro="multiple_input_bams" />
-
-        <conditional name="advancedOpt">
-            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
-            </param>
-            <when value="no" />
-            <when value="yes">
-                <param argument="--numberOfSamples" type="integer" value="100000" min="1"
-                   label="Number of samples"
-                   help="Number of samples taken from the genome to compute the scaling factors."/>
-                <expand macro="region_limit_operation" />
-                <expand macro="read_processing_options" />
-                <expand macro="skipZeros" />
-                <expand macro="plotTitle" />
-                <expand macro="blacklist" />
-            </when>
-        </conditional>
-
-        <expand macro="input_image_file_format" />
-        <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
-
-
-    </inputs>
-    <outputs>
-        <expand macro="output_image_file_format_not_nested" />
-        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
-            <filter>outRawCounts is True</filter>
-        </data>
-    </outputs>
-    <tests>
-        <test>
-            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
-            <!--param name="outFileFormat" value="png" /-->
-            <param name="showAdvancedOpt" value="yes" />
-            <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="2400" />
-        </test>
-    </tests>
-    <help>
-<![CDATA[
-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
----------
-
-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:: $PATH_TO_IMAGES/plotCoverage_annotated.png
-   :width: 600
-   :height: 291
-
-
-@REFERENCES@
-]]>
-    </help>
-    <expand macro="citations" />
-</tool>
+<tool id="deeptools_plot_coverage" name="plotCoverage" version="@WRAPPER_VERSION@.0">
+    <description>assesses the sequencing depth of BAM files </description>
+    <macros>
+        <token name="@BINARY@">plotCoverage</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command>
+<![CDATA[
+        #set files=[]
+        #set labels=[]
+
+        @multiple_input_bams@
+
+        @BINARY@
+
+            @THREADS@
+
+            --plotFile '$outFileName'
+            --bamfiles #echo " ".join($files)#
+            --labels #echo " ".join($labels)#
+            --plotFileFormat "$outFileFormat"
+
+            #if $outRawCounts:
+                --outRawCounts '$outFileRawCounts'
+            #end if
+
+            #if $advancedOpt.showAdvancedOpt == "yes":
+                --numberOfSamples '$advancedOpt.numberOfSamples'
+                $advancedOpt.skipZeros
+
+                #if str($advancedOpt.region).strip() != '':
+                    --region '$advancedOpt.region'
+                #end if
+                --numberOfSamples $advancedOpt.numberOfSamples
+
+                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
+                    --plotTitle '$advancedOpt.plotTitle'
+                #end if
+                @ADVANCED_OPTS_READ_PROCESSING@
+                @blacklist@
+            #end if
+
+]]>
+    </command>
+    <inputs>
+
+        <expand macro="multiple_input_bams" />
+
+        <conditional name="advancedOpt">
+            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param argument="--numberOfSamples" type="integer" value="100000" min="1"
+                   label="Number of samples"
+                   help="Number of samples taken from the genome to compute the scaling factors."/>
+                <expand macro="region_limit_operation" />
+                <expand macro="read_processing_options" />
+                <expand macro="skipZeros" />
+                <expand macro="plotTitle" />
+                <expand macro="blacklist" />
+            </when>
+        </conditional>
+
+        <expand macro="input_image_file_format" />
+        <param argument="--outRawCounts" type="boolean" label="Save raw counts (coverages) to a file" help=""/>
+
+
+    </inputs>
+    <outputs>
+        <expand macro="output_image_file_format_not_nested" />
+        <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
+            <filter>outRawCounts is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
+            <!--param name="outFileFormat" value="png" /-->
+            <param name="showAdvancedOpt" value="yes" />
+            <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="2400" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+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
+---------
+
+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@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r 4ae546bddd00 -r 94b05ea80203 test-data/bamCompare_result2.bw
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/bamCoverage_result1.bw
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/bamCoverage_result2.bw
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/bamCoverage_result6.bw
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/bamPEFragmentSize_histogram_result1.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/bigwigCompare_result1.bw
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/computeMatrixOperations.txt
--- a/test-data/computeMatrixOperations.txt	Tue Jan 24 04:56:34 2017 -0500
+++ b/test-data/computeMatrixOperations.txt	Fri Mar 31 09:26:58 2017 -0400
@@ -1,4 +1,4 @@
 Groups:
 	genes
 Samples:
-	file_0
+	bamCoverage_result4_bw_0
diff -r 4ae546bddd00 -r 94b05ea80203 test-data/computeMatrixOperations_result2.mat.gz
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/computeMatrix_result1.gz
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/computeMatrix_result2.gz
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/computeMatrix_result3.gz
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/correctGCBias_result1.bam
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/heatmapper_result1.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/heatmapper_result2.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/multiBamSummary_result1.npz
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/multiBamSummary_result2.npz
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/multiBamSummary_result2b.npz
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/multiBigwigSummary_result1.npz
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/plotCorrelation_result1.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/plotCorrelation_result1.tabular
--- a/test-data/plotCorrelation_result1.tabular	Tue Jan 24 04:56:34 2017 -0500
+++ b/test-data/plotCorrelation_result1.tabular	Fri Mar 31 09:26:58 2017 -0400
@@ -1,3 +1,3 @@
-	'bowtie2-test1.bam'	'bowtie2-test1.bam'
-'bowtie2-test1.bam'	1.0000	1.0000
-'bowtie2-test1.bam'	1.0000	1.0000
+	'bowtie2 test1.bam'	'bowtie2 test1.bam'
+'bowtie2 test1.bam'	1.0000	1.0000
+'bowtie2 test1.bam'	1.0000	1.0000
diff -r 4ae546bddd00 -r 94b05ea80203 test-data/plotCorrelation_result2.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/plotCoverage_result1.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/plotEnrichment_output.png
Binary file test-data/plotEnrichment_output.png has changed
diff -r 4ae546bddd00 -r 94b05ea80203 test-data/plotFingerprint_quality_metrics.tabular
--- a/test-data/plotFingerprint_quality_metrics.tabular	Tue Jan 24 04:56:34 2017 -0500
+++ b/test-data/plotFingerprint_quality_metrics.tabular	Fri Mar 31 09:26:58 2017 -0400
@@ -1,3 +1,3 @@
 Sample	AUC	Synthetic AUC	X-intercept	Synthetic X-intercept	Elbow Point	Synthetic Elbow Point	JS Distance	Synthetic JS Distance	% genome enriched	diff. enrichment	CHANCE divergence
-bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269861238192	NA	NA	NA
-bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269861238192	NA	NA	NA
+bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269004498068	NA	NA	NA
+bowtie2 test1.bam	0.00493632029864	0.481650684758	0.984443061605	1.15310443503e-24	0.984940883634	0.523268829811	NA	0.269004498068	NA	NA	NA
diff -r 4ae546bddd00 -r 94b05ea80203 test-data/plotFingerprint_result1.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/plotFingerprint_result2.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/profiler_result1.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/profiler_result2.png
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diff -r 4ae546bddd00 -r 94b05ea80203 test-data/profiler_result2.tabular
--- a/test-data/profiler_result2.tabular	Tue Jan 24 04:56:34 2017 -0500
+++ b/test-data/profiler_result2.tabular	Fri Mar 31 09:26:58 2017 -0400
@@ -1,3 +1,3 @@
 bin labels		-0.0Kb	0.0Kb
 bins		1	2
-file_0	genes	2477942.34473	2610259.65234
+bamCoverage_result4_bw_0	genes	2477942.875	2610260.125
diff -r 4ae546bddd00 -r 94b05ea80203 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jan 24 04:56:34 2017 -0500
+++ b/tool_dependencies.xml	Fri Mar 31 09:26:58 2017 -0400
@@ -1,7 +1,7 @@
 <?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" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="bd7165ea6526" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="deeptools" version="2.4.2">
         <repository changeset_revision="efc55c226f11" name="package_python_2_7_deeptools_2_4_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />