# HG changeset patch
# User bgruening
# Date 1579851154 0
# Node ID 7f7a2ae8a3107aea6b8dd691907ae8812902e5c1
# Parent  7f265e1ced94e40962be7acc495961adda41fdb7
"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"

diff -r 7f265e1ced94 -r 7f7a2ae8a310 datatypes_conf.xml
--- a/datatypes_conf.xml	Tue Apr 02 07:07:33 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 7f265e1ced94 -r 7f7a2ae8a310 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Apr 02 07:07:33 2019 -0400
+++ b/deepTools_macros.xml	Fri Jan 24 07:32:34 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 7f265e1ced94 -r 7f7a2ae8a310 plotCorrelation.xml
--- a/plotCorrelation.xml	Tue Apr 02 07:07:33 2019 -0400
+++ b/plotCorrelation.xml	Fri Jan 24 07:32:34 2020 +0000
@@ -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 7f265e1ced94 -r 7f7a2ae8a310 readme.rst
--- a/readme.rst	Tue Apr 02 07:07:33 2019 -0400
+++ b/readme.rst	Fri Jan 24 07:32:34 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 7f265e1ced94 -r 7f7a2ae8a310 repository_dependencies.xml
--- a/repository_dependencies.xml	Tue Apr 02 07:07:33 2019 -0400
+++ b/repository_dependencies.xml	Fri Jan 24 07:32:34 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 7f265e1ced94 -r 7f7a2ae8a310 test-data/heatmapper_result1.png
Binary file test-data/heatmapper_result1.png has changed
diff -r 7f265e1ced94 -r 7f7a2ae8a310 test-data/heatmapper_result2.png
Binary file test-data/heatmapper_result2.png has changed
diff -r 7f265e1ced94 -r 7f7a2ae8a310 test-data/plotCoverage.metrics
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/plotCoverage.metrics	Fri Jan 24 07:32:34 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 7f265e1ced94 -r 7f7a2ae8a310 test-data/plotCoverage_result1.png
Binary file test-data/plotCoverage_result1.png has changed