# HG changeset patch
# User iuc
# Date 1494343138 14400
# Node ID 9129584416e24e4992bd27238ddfa73e8796cb17
# Parent  bb40e4252392b88cfe055dd31ca19e3dc852b19b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

diff -r bb40e4252392 -r 9129584416e2 macros.xml
--- a/macros.xml	Tue Dec 01 16:12:16 2015 -0500
+++ b/macros.xml	Tue May 09 11:18:58 2017 -0400
@@ -1,16 +1,17 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.2">samtools</requirement>
+            <requirement type="package" version="1.3.1">samtools</requirement>
             <yield/>
         </requirements>
     </xml>
+    <token name="@TOOL_VERSION@">1.3.1</token>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
                 @misc{SAM_def,
                 title={Definition of SAM/BAM format},
-                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+                url = {https://samtools.github.io/hts-specs/},}
             </citation>
             <citation type="doi">10.1093/bioinformatics/btp352</citation>
             <citation type="doi">10.1093/bioinformatics/btr076</citation>
@@ -41,7 +42,7 @@
         </citations>
     </xml>
     <xml name="version_command">
-        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+        <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
     </xml>
     <xml name="stdio">
         <stdio>
@@ -64,7 +65,5 @@
 5. Click **Save**
 
 The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
-
     </token>
-
 </macros>
diff -r bb40e4252392 -r 9129584416e2 samtools_rmdup.xml
--- a/samtools_rmdup.xml	Tue Dec 01 16:12:16 2015 -0500
+++ b/samtools_rmdup.xml	Tue May 09 11:18:58 2017 -0400
@@ -1,56 +1,56 @@
-<tool id="samtools_rmdup" name="RmDup" version="2.0">
-  <description>remove PCR duplicates</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <requirements>
-    <requirement type="package" version="0.1.19">samtools</requirement>
-  </requirements>
-  <expand macro="stdio"></expand>
-  <expand macro="version_command"></expand>
-  <command>samtools rmdup 
-  #if str( $bam_paired_end_type.bam_paired_end_type_selector ) == "PE"
-      ${bam_paired_end_type.force_se}
-  #else:
-      -s
-  #end if
-  "$input1" "$output1"
-  </command>
-  <inputs>
-    <param name="input1" type="data" format="bam" label="BAM File" />
-    
-    <conditional name="bam_paired_end_type">
-      <param name="bam_paired_end_type_selector" type="select" label="Is this paired-end or single end data">
-        <option value="PE" selected="True">BAM is paired-end</option>
-        <option value="SE">BAM is single-end (-s)</option>
-      </param>
-      <when value="PE">
-        <param name="force_se" type="boolean" label="Treat as single-end" help="-S" truevalue="-S" falsevalue="" checked="False"/>
-      </when>
-      <when value="SE" /> <!-- No extra parameters here -->
-    </conditional>
-    
-  </inputs>
-  <outputs>
-    <data name="output1" format="bam" />
-  </outputs>
-  <tests>
-    <test>
-      <param name="input1" value="samtools-rmdup-input1.bam" ftype="bam" />
-      <param name="bam_paired_end_type_selector" value="PE" />
-      <param name="force_se" />
-      <output name="output1" file="samtools-rmdup-test1.bam" ftype="bam" sort="True" />
-    </test>
-  </tests>
-  <help>
+<tool id="samtools_rmdup" name="RmDup" version="2.0.1">
+    <description>remove PCR duplicates</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <expand macro="requirements" />
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+
+    <command><![CDATA[
+    samtools rmdup
+        #if str( $bam_paired_end_type.bam_paired_end_type_selector ) == "PE"
+            ${bam_paired_end_type.force_se}
+        #else:
+            -s
+        #end if
+        '$input1'
+        '$output1'
+    ]]></command>
+
+    <inputs>
+        <param name="input1" type="data" format="bam" label="BAM File" />
 
+        <conditional name="bam_paired_end_type">
+            <param name="bam_paired_end_type_selector" type="select" label="Is this paired-end or single end data">
+                <option value="PE" selected="True">BAM is paired-end</option>
+                <option value="SE">BAM is single-end (-s)</option>
+            </param>
+            <when value="PE">
+                <param name="force_se" argument="-S" type="boolean" truevalue="-S" falsevalue="" checked="False" label="Treat as single-end"/>
+            </when>
+            <when value="SE" /> <!-- No extra parameters here -->
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data name="output1" format="bam" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input1" value="samtools-rmdup-input1.bam" ftype="bam" />
+            <param name="bam_paired_end_type_selector" value="PE" />
+            <param name="force_se" />
+
+            <output name="output1" file="samtools-rmdup-test1.bam" ftype="bam" sort="True" />
+        </test>
+    </tests>
+    <help>
 **What it does**
 
-Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads). This tool has the following parameters::
-
-  -s    rmdup for SE reads
-  -S    treat PE reads as SE in rmdup (force -s)
-
-  </help>
-    <expand macro="citations"></expand>
+Remove potential PCR duplicates: if multiple read pairs have identical external coordinates, only retain the pair with highest mapping quality. In the paired-end mode, this command ONLY works with FR orientation and requires ISIZE is correctly set. It does not work for unpaired reads (e.g. two ends mapped to different chromosomes or orphan reads).
+    </help>
+    <expand macro="citations"/>
 </tool>
diff -r bb40e4252392 -r 9129584416e2 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 01 16:12:16 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>