# HG changeset patch
# User bgruening
# Date 1534884555 14400
# Node ID e074335bde9c3511cc2966452af7301d14ab6942
# Parent  528355f62f3a712dca8b0529e0587b8520ec5b08
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

diff -r 528355f62f3a -r e074335bde9c deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:42:13 2018 -0400
+++ b/deepTools_macros.xml	Tue Aug 21 16:49:15 2018 -0400
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.0.2</token>
+    <token name="@WRAPPER_VERSION@">3.1.2.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.0.2">deeptools</requirement>
+            <requirement type="package" version="3.1.2">deeptools</requirement>
             <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -216,7 +216,7 @@
             label="Use a metagene model"
             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="trascript designator"
+            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" />
         <param argument="--exonID" optional="True" value="exon" type="text"
             label="exon designator"
@@ -603,6 +603,18 @@
                  (default: False)" />
     </xml>
 
+    <xml name="exactScaling">
+        <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
+            label="Compute an exact scaling factor"
+            help="Compute an exact scaling factor rather than one based on
+                  sampled reads. This is only useful in cases where you are
+                  filtering some alignments out AND this are both rare and
+                  tend to clump together in the genome. In such cases the
+                  region-based sampling employed by deepTools would produce
+                  inaccurate scaling factors. Note that this option results
+                  in the process taking significantly more time to complete." />
+    </xml>
+
     <xml name="input_save_matrix_values">
         <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
     </xml>
@@ -642,7 +654,7 @@
     </xml>
 
     <xml name="output_image_file_format">
-        <data format="png" name="outFileName" label="${tool.name} image">
+        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
             <change_format>
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
                 <when input="output.outFileFormat" value="svg" format="svg" />
@@ -653,7 +665,7 @@
     </xml>
 
     <xml name="output_image_file_format_not_nested">
-        <data format="png" name="outFileName" label="${tool.name} image">
+        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
             <change_format>
                 <when input="outFileFormat" value="pdf" format="pdf" />
                 <when input="outFileFormat" value="svg" format="svg" />
diff -r 528355f62f3a -r e074335bde9c plotPCA.xml
--- a/plotPCA.xml	Thu Apr 05 10:42:13 2018 -0400
+++ b/plotPCA.xml	Tue Aug 21 16:49:15 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0">
+<tool id="deeptools_plot_pca" name="plotPCA" version="@WRAPPER_VERSION@.0" profile="18.01">
     <description>Generate principal component analysis (PCA) plots from multiBamSummary or multiBigwigSummary output</description>
     <macros>
         <token name="@BINARY@">plotPCA</token>
@@ -22,6 +22,9 @@
                 #if $advancedOpt.colors:
                     --colors $advancedOpt.colors
                 #end if
+                #if $advancedOpt.markers:
+                    --markers $advancedOpt.markers
+                #end if
             #end if
             #if $outFileNameData
                 --outFileNameData '$output_outFileNameData'
@@ -40,7 +43,7 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <expand macro="plotWidthHeight" PLOTWIDTH="5.0" PLOTHEIGHT="10.0" />
+                <expand macro="plotWidthHeight" PLOTWIDTH="10.0" PLOTHEIGHT="10.0" />
                 <param name="PCs" argument="--PCs" label="Principal components to plot" value="1 2" type="text"
                     help="The principal components to plot. If specified, you must provide two different integers, greater than zero, separated by a space. An example (and the default) is '1 2'." />
                 <param name="ntop" argument="--ntop" label="Number of rows to use" value="1000" type="integer"
@@ -50,6 +53,8 @@
                 <param argument="--rowCenter" type="boolean" label="Center Rows?" help="When specified, each row (bin, gene, etc.) in the matrix is centered at 0 before the PCA is computed. This is useful only if you have a strong bin/gene/etc. correlation and the resulting principal component has samples stacked vertically. This option is not applicable if the PCA is performed on the transposed matrix." truevalue="--rowCenter" falsevalue="" />
                 <param argument="--colors" type="text" name="colors" label="Symbol colors" value="" optional="True"
                     help="A list of colors for the symbols. Color names and html hex string (e.g., #eeff22) are accepted. The color names should be space separated. For example, --colors 'red blue green'. If not specified, the symbols will be given automatic colors." />
+                <param argument="--markers" type="text" name="markers" label="Custom markers" value="" optional="True"
+                    help="A list of markers for the symbols. (e.g., '&lt;','&gt;','o') are accepted. The marker values should be space separated. For example, 's' 'o' 's' 'o'. If not specified, the symbols will be given automatic shapes." />
             </when>
         </conditional>
     </inputs>
diff -r 528355f62f3a -r e074335bde9c test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 528355f62f3a -r e074335bde9c test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed