# HG changeset patch
# User bgruening
# Date 1579851630 0
# Node ID 2c17ceeae363ea15de572f8e0494139d85e0826b
# Parent  ed617a38a03ed2a0cf20c83038c585f3bfc452ab
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"

diff -r ed617a38a03e -r 2c17ceeae363 datatypes_conf.xml
--- a/datatypes_conf.xml	Tue Apr 02 07:09:04 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-    <registration>
-        <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
-        <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="True" display_in_upload="True"/>
-    </registration>
-</datatypes>
diff -r ed617a38a03e -r 2c17ceeae363 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Apr 02 07:09:04 2019 -0400
+++ b/deepTools_macros.xml	Fri Jan 24 07:40:30 2020 +0000
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.2.1.0</token>
+    <token name="@WRAPPER_VERSION@">3.3.2.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.2.1">deeptools</requirement>
+            <requirement type="package" version="3.3.2">deeptools</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -164,6 +164,12 @@
                     </when>
                     <when value="none" />
                 </conditional>
+                <param argument="--silhouette" type="boolean" truevalue="--silhouette" falsevalue=""
+                    label="Compute the silhouette score for each region"
+                    help="Compute the silhouette score for regions. This is only applicable if clustering has been performed.
+                    The silhouette score is a measure of how similar a region is to other regions in the same cluster as
+                    opposed to those in other clusters. It will be reported in the final column of the BED file with regions.
+                    The silhouette evaluation can be very slow when you have more than 100 000 regions." />
             </when>
             <when value="yes" />
         </conditional>
@@ -181,6 +187,7 @@
                     --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
                 #end if
             #end if
+            $advancedOpt.used_multiple_regions.silhouette
         #end if
     </token>
 
@@ -217,10 +224,10 @@
             help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
         <param argument="--transcriptID" optional="True" value="transcript" type="text"
             label="transcript designator"
-            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
+            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as transcripts. Default: transcript" />
         <param argument="--exonID" optional="True" value="exon" type="text"
             label="exon designator"
-            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
+            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 3) will be processed as exons. CDS would be another common value for this. Default: exon" />
         <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
             label="transcriptID key designator"
             help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
@@ -368,10 +375,12 @@
 
 For more information on the tools, please visit our `help site`_.
 
-If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
+For support or questions please post to `Biostars`_. For bug reports and feature requests please open an issue `on github`_.
 
 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
 
+.. _Biostars: http://biostars.org
+.. _on github: http://github.com
 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
 .. _help site: https://deeptools.readthedocs.org/
@@ -824,6 +833,23 @@
             <option value="brg">brg</option>
             <option value="jet">jet</option>
             <option value="afmhot">afmhot</option>
+            <option value="Wistia">Wistia</option>
+            <option value="cividis">cividis</option>
+            <option value="icefire">icefire</option>
+            <option value="inferno">inferno</option>
+            <option value="magma">magma</option>
+            <option value="mako">mako</option>
+            <option value="nipy_spectral">nipy_spectral</option>
+            <option value="plasma">plasma</option>
+            <option value="rocket">rocket</option>
+            <option value="tab10">tab10</option>
+            <option value="tab20">tab20</option>
+            <option value="tab20b">tab20b</option>
+            <option value="tab20c">tab20c</option>
+            <option value="twilight">twilight</option>
+            <option value="twilight_shifted">twilight_shifted</option>
+            <option value="viridis">viridis</option>
+            <option value="vlag">vlag</option>
             <option value="Accent_r">Accent reversed</option>
             <option value="Spectral_r">Spectral reversed</option>
             <option value="Set1_r">Set1 reversed</option>
@@ -893,6 +919,23 @@
             <option value="brg_r">brg reversed</option>
             <option value="jet_r">jet reversed</option>
             <option value="afmhot_r">afmhot reversed</option>
+            <option value="Wistia_r">Wistia reversed</option>
+            <option value="cividis_r">cividis reversed</option>
+            <option value="icefire_r">icefire reversed</option>
+            <option value="inferno_r">inferno reversed</option>
+            <option value="magma_r">magma reversed</option>
+            <option value="mako_r">mako reversed</option>
+            <option value="nipy_spectral_r">nipy_spectral reversed</option>
+            <option value="plasma_r">plasma reversed</option>
+            <option value="rocket_r">rocket reversed</option>
+            <option value="tab10_r">tab10 reversed</option>
+            <option value="tab20_r">tab20 reversed</option>
+            <option value="tab20b_r">tab20b reversed</option>
+            <option value="tab20c_r">tab20c reversed</option>
+            <option value="twilight_r">twilight reversed</option>
+            <option value="twilight_shifted_r">twilight_shifted reversed</option>
+            <option value="viridis_r">viridis reversed</option>
+            <option value="vlag_r">vlag reversed</option>
         </param>
 
     </xml>
diff -r ed617a38a03e -r 2c17ceeae363 plotCoverage.xml
--- a/plotCoverage.xml	Tue Apr 02 07:09:04 2019 -0400
+++ b/plotCoverage.xml	Fri Jan 24 07:40:30 2020 +0000
@@ -25,6 +25,23 @@
                 --outRawCounts '$outFileRawCounts'
             #end if
 
+            #if ' '.join(map(str, $BED)) != 'None':
+                #set bedFileLList=[]
+                #for $f in $BED:
+                    #silent $bedFileList.append("'%s'" % $f)
+                #end for
+                #if $bedFileList != ["'None'"]:
+                    --BED #echo ' '.join($bedFileList)#
+                #end if
+            #end if
+
+            #if $coverageOpt.showCoverageOpt == "yes":
+                --outCoverageMetrics '$outFileCoverageMetrics'
+                #for $t in $coverageOpt.thresholds:
+                    -ct $t.coverageThreshold
+                #end for
+            #end if
+
             #if $advancedOpt.showAdvancedOpt == "yes":
                 --numberOfSamples '$advancedOpt.numberOfSamples'
                 $advancedOpt.skipZeros
@@ -48,11 +65,28 @@
 
         <expand macro="multiple_input_bams" MIN="1"/>
         <expand macro="custom_sample_labels" />
+        <param argument="--BED" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
+            label="Regions of interest"
+            help="Limits the coverage analysis to the regions specified in these files. This overrides --numberOfSamples. It is inadvisable to combine this with saving the raw counts." />
+
+        <conditional name="coverageOpt">
+            <param name="showCoverageOpt" type="select" label="Show coverage metrics options">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param argument="--outCoverageMetrics" type="boolean" label="Save per-threshold coverage metrics?"/>
+                <repeat name="thresholds" title="Coverage Thresholds">
+                    <param argument="--coverageThreshold" type="integer" min="0" label="Coverage Threshold" value="0"/>
+                </repeat>
+            </when>
+        </conditional>
 
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
-                <option value="no" selected="true">no</option>
-                <option value="yes">yes</option>
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
             </param>
             <when value="no" />
             <when value="yes">
@@ -78,6 +112,9 @@
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
             <filter>outRawCounts is True</filter>
         </data>
+        <data format="tabular" name="outFileCoverageMetrics" label="${tool.name} on ${on_string}: Threshold Metrics">
+            <filter>coverageOpt.outCoverageMetrics is True</filter>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -89,6 +126,18 @@
             <output name="outFileRawCounts" file="plotCoverage_result1.tabular" ftype="tabular" />
             <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
         </test>
+        <test>
+            <param name="bamfiles" value="bowtie2 test1.bam,bowtie2 test1.bam" ftype="bam" />
+            <param name="showAdvancedOpt" value="yes" />
+            <param name="plotTitle" value="Test Title from Galaxy" />
+            <param name="showCoverageOpt" value="yes" />
+            <param name="coverageThreshold" value="0" />
+            <param name="coverageThreshold" value="5" />
+            <param name="coverageThreshold" value="10" />
+            <param name="coverageThreshold" value="20" />
+            <output name="outFileName" file="plotCoverage_result1.png" ftype="png" compare="sim_size" delta="2400" />
+            <output name="outFileCoverageMetrics" file="plotCoverage.metrics" ftype="tabular" />
+        </test>
     </tests>
     <help>
 <![CDATA[
diff -r ed617a38a03e -r 2c17ceeae363 readme.rst
--- a/readme.rst	Tue Apr 02 07:09:04 2019 -0400
+++ b/readme.rst	Fri Jan 24 07:40:30 2020 +0000
@@ -22,7 +22,7 @@
 
     https://github.com/deeptools/deepTools
 
-For support, questions, or feature requests contact: deeptools@googlegroups.com
+For support or questions please post to `Biostars <http://biostars.org>`__. For bug reports and feature requests please open an issue `<on github <http://github.com/deeptools/deeptools>`__.
 
 
 ============
diff -r ed617a38a03e -r 2c17ceeae363 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Apr 02 07:09:04 2019 -0400
+++ b/repository_dependencies.xml	Fri Jan 24 07:40:30 2020 +0000
@@ -1,4 +1,4 @@
 <?xml version="1.0" ?>
 <repositories>
-    <repository changeset_revision="fced964b054a" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="b640d79b49cb" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
 </repositories>
\ No newline at end of file
diff -r ed617a38a03e -r 2c17ceeae363 test-data/heatmapper_result1.png
Binary file test-data/heatmapper_result1.png has changed
diff -r ed617a38a03e -r 2c17ceeae363 test-data/heatmapper_result2.png
Binary file test-data/heatmapper_result2.png has changed
diff -r ed617a38a03e -r 2c17ceeae363 test-data/plotCoverage.metrics
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage.metrics	Fri Jan 24 07:40:30 2020 +0000
@@ -0,0 +1,9 @@
+Sample	Threshold	Percent
+bowtie2 test1.bam	0	100.000
+bowtie2 test1.bam	0	100.000
+bowtie2 test1.bam	5	 1.509
+bowtie2 test1.bam	5	 1.509
+bowtie2 test1.bam	10	 1.461
+bowtie2 test1.bam	10	 1.461
+bowtie2 test1.bam	20	 1.406
+bowtie2 test1.bam	20	 1.406
diff -r ed617a38a03e -r 2c17ceeae363 test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed