# HG changeset patch
# User bgruening
# Date 1579850120 0
# Node ID f586a973f94e791343dd82551c6d0564b37e195c
# Parent  c0b1a96ba39a1a9a84ff9ab6737b5f7aa1abfaa1
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"

diff -r c0b1a96ba39a -r f586a973f94e datatypes_conf.xml
--- a/datatypes_conf.xml	Tue Apr 02 07:05:03 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 c0b1a96ba39a -r f586a973f94e deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Apr 02 07:05:03 2019 -0400
+++ b/deepTools_macros.xml	Fri Jan 24 07:15:20 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 c0b1a96ba39a -r f586a973f94e readme.rst
--- a/readme.rst	Tue Apr 02 07:05:03 2019 -0400
+++ b/readme.rst	Fri Jan 24 07:15:20 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 c0b1a96ba39a -r f586a973f94e repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Apr 02 07:05:03 2019 -0400
+++ b/repository_dependencies.xml	Fri Jan 24 07:15:20 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 c0b1a96ba39a -r f586a973f94e test-data/heatmapper_result1.png
Binary file test-data/heatmapper_result1.png has changed
diff -r c0b1a96ba39a -r f586a973f94e test-data/heatmapper_result2.png
Binary file test-data/heatmapper_result2.png has changed
diff -r c0b1a96ba39a -r f586a973f94e test-data/plotCoverage.metrics
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage.metrics	Fri Jan 24 07:15:20 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 c0b1a96ba39a -r f586a973f94e test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed