# HG changeset patch
# User bgruening
# Date 1534882821 14400
# Node ID 016d5740d5f5d99d35afd6b2bad9b6d33643d2cc
# Parent  56cc6180673d7fc45f1a573e4eae16c8eb0c9265
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

diff -r 56cc6180673d -r 016d5740d5f5 bamPEFragmentSize.xml
--- a/bamPEFragmentSize.xml	Thu Apr 05 10:38:56 2018 -0400
+++ b/bamPEFragmentSize.xml	Tue Aug 21 16:20:21 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
+<tool id="deeptools_bam_pe_fragmentsize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0" profile="18.01">
     <description>Estimate the predominant cDNA fragment length from paired-end sequenced BAM/CRAM files</description>
     <macros>
         <token name="@BINARY@">bamPEFragmentSize</token>
diff -r 56cc6180673d -r 016d5740d5f5 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:38:56 2018 -0400
+++ b/deepTools_macros.xml	Tue Aug 21 16:20:21 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 56cc6180673d -r 016d5740d5f5 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 56cc6180673d -r 016d5740d5f5 test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed