changeset 1:b7f7826ef1cd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40

--- a/macros.xml	Tue Apr 21 17:44:16 2015 -0400
+++ b/macros.xml	Tue May 09 11:18:30 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>

--- a/samtools_split.xml	Tue Apr 21 17:44:16 2015 -0400
+++ b/samtools_split.xml	Tue May 09 11:18:30 2017 -0400
@@ -1,26 +1,26 @@
-<tool id="samtools_split" name="Split" version="1.1">
+<tool id="samtools_split" name="Split" version="@TOOL_VERSION@">
     <description>BAM dataset on readgroups</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements"></expand>
-    <expand macro="stdio"></expand>
-    <expand macro="version_command"></expand>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
     <command><![CDATA[
         samtools split -f 'Read_Group_%!.bam'
         #if $header:
-            -u "${output}":"${header}"
+            -u '${output}:${header}'
         #else:
-            -u "${output}"
+            -u '${output}'
         #end if
         "${input_bam}"
-        ]]></command>
+    ]]></command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="BAM file" />
-        <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" />
+        <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" />
      </inputs>
     <outputs>
-        <data format="bam" name="output" label="${tool.name} on ${on_string}">
+        <data name="output" format="bam" label="${tool.name} on ${on_string}">
             <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" />
         </data>
     </outputs>
@@ -34,14 +34,12 @@
             </output>
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 Splits BAM files on readgroups.
 
-This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. 
-
-    </help>
-    <expand macro="citations"></expand>
+This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset.
+    ]]></help>
+    <expand macro="citations"/>
 </tool>
-

--- a/tool_dependencies.xml	Tue Apr 21 17:44:16 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="samtools" version="1.2">
-        <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>