# HG changeset patch
# User bgruening
# Date 1579944263 18000
# Node ID 32e451def88cbd4c273c4165526db2d8056117a2
# Parent  bd7db9e2f2cb4972ee5498a1f20a423def6dccb3
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"

diff -r bd7db9e2f2cb -r 32e451def88c datatypes_conf.xml
--- a/datatypes_conf.xml	Wed May 29 09:42:57 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 bd7db9e2f2cb -r 32e451def88c deepTools_macros.xml
--- a/deepTools_macros.xml	Wed May 29 09:42:57 2019 -0400
+++ b/deepTools_macros.xml	Sat Jan 25 04:24:23 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 bd7db9e2f2cb -r 32e451def88c plotCorrelation.xml
--- a/plotCorrelation.xml	Wed May 29 09:42:57 2019 -0400
+++ b/plotCorrelation.xml	Sat Jan 25 04:24:23 2020 -0500
@@ -18,11 +18,11 @@
                 --plotHeight $plotting_type.plotHeight
             #else:
                 --plotTitle '$plotting_type.plotTitle'
-                #if str($plotting_type.xRange) != '':
-                    --xRange '$plotting_type.xRange'
+                #if str($plotting_type.xrange_conditional.xrange_select) == 'yes':
+                    --xRange $plotting_type.xrange_conditional.xRange_min $plotting_type.xrange_conditional.xRange_max
                 #end if
-                #if str($plotting_type.yRange) != '':
-                    --yRange '$plotting_type.yRange'
+                #if str($plotting_type.yrange_conditional.yrange_select) == 'yes':
+                    --yRange $plotting_type.yrange_conditional.yRange_min $plotting_type.yrange_conditional.yRange_max
                 #end if
                 $plotting_type.log1p
             #end if
@@ -50,12 +50,32 @@
             </when>
             <when value="scatterplot">
                 <expand macro="plotTitle" />
-                <param argument="--xRange" type="text" value="" optional="true"
-                    label="X axis range"
-                    help="X axis range, the default scales these such that the full range of dots is displayed. The input should be two integers separated by a space." />
-                <param argument="--yRange" type="text" value="" optional="true"
-                    label="Y axis range"
-                    help="Y axis range, the default scales these such that the full range of dots is displayed. The input should be two integers separated by a space." />
+                <conditional name="xrange_conditional">
+                    <param type="select" name="xrange_select" label="Manually set X axis range?">
+                        <option value="no" selected="True">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="yes">
+                        <param name="xRange_min" type="integer" value="0" label="X axis minimum value"
+                            help="X axis minimum value. Not specifying this scales these such that the full range of dots is displayed." />
+                        <param name="xRange_max" type="integer" value="1000" label="X axis maximum value"
+                            help="X axis maximum value. Not specifying this scales these such that the full range of dots is displayed." />
+                    </when>
+                    <when value="no" />
+                </conditional>
+                <conditional name="yrange_conditional">
+                    <param type="select" name="yrange_select" label="Manually set Y axis range?">
+                        <option value="no" selected="True">No</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="yes">
+                        <param name="yRange_min" type="integer" value="0" label="Y axis minimum value"
+                            help="Y axis minimum value. Not specifying this scales these such that the full range of dots is displayed." />
+                        <param name="yRange_max" type="integer" value="1000" label="Y axis maximum value"
+                            help="Y axis maximum value. Not specifying this scales these such that the full range of dots is displayed." />
+                    </when>
+                    <when value="no" />
+                </conditional>
                 <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue=""
                     label="Log transform"
                     help="Plot the natural log of the scatter plot after adding 1. Note that this is ONLY for plotting, the correlation is unaffected." />
diff -r bd7db9e2f2cb -r 32e451def88c readme.rst
--- a/readme.rst	Wed May 29 09:42:57 2019 -0400
+++ b/readme.rst	Sat Jan 25 04:24:23 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 bd7db9e2f2cb -r 32e451def88c repository_dependencies.xml
--- a/repository_dependencies.xml	Wed May 29 09:42:57 2019 -0400
+++ b/repository_dependencies.xml	Sat Jan 25 04:24:23 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 bd7db9e2f2cb -r 32e451def88c test-data/heatmapper_result1.png
Binary file test-data/heatmapper_result1.png has changed
diff -r bd7db9e2f2cb -r 32e451def88c test-data/heatmapper_result2.png
Binary file test-data/heatmapper_result2.png has changed