# HG changeset patch
# User bgruening
# Date 1579945668 18000
# Node ID e821645ef8fc8ae690f9cc52ce3c5127c10e6fbc
# Parent  268e91e540ee259ecb4da3cc02c4be975c17c9e2
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"

diff -r 268e91e540ee -r e821645ef8fc datatypes_conf.xml
--- a/datatypes_conf.xml	Wed May 29 09:46:17 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 268e91e540ee -r e821645ef8fc deepTools_macros.xml
--- a/deepTools_macros.xml	Wed May 29 09:46:17 2019 -0400
+++ b/deepTools_macros.xml	Sat Jan 25 04:47:48 2020 -0500
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.3.0.0</token>
+    <token name="@WRAPPER_VERSION@">3.3.2.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.3.0">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 268e91e540ee -r e821645ef8fc readme.rst
--- a/readme.rst	Wed May 29 09:46:17 2019 -0400
+++ b/readme.rst	Sat Jan 25 04:47:48 2020 -0500
@@ -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 268e91e540ee -r e821645ef8fc repository_dependencies.xml
--- a/repository_dependencies.xml	Wed May 29 09:46:17 2019 -0400
+++ b/repository_dependencies.xml	Sat Jan 25 04:47:48 2020 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0" ?>
 <repositories>
-    <repository changeset_revision="9946bc39c834" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="16c0c73b28ad" name="data_manager_twobit_builder" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/>
 </repositories>
\ No newline at end of file
diff -r 268e91e540ee -r e821645ef8fc test-data/heatmapper_result1.png
Binary file test-data/heatmapper_result1.png has changed
diff -r 268e91e540ee -r e821645ef8fc test-data/heatmapper_result2.png
Binary file test-data/heatmapper_result2.png has changed