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diff samtools_sort.xml @ 1:cab3f8d35989 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:18:12 -0400
parents a430da4f04cd
children f56bdb93ae58
line wrap: on
line diff
--- a/samtools_sort.xml	Tue Apr 21 17:41:18 2015 -0400
+++ b/samtools_sort.xml	Tue May 09 11:18:12 2017 -0400
@@ -1,12 +1,20 @@
-<tool id="samtools_sort" name="Sort" version="2.0">
-    <description>BAM dataset</description>
+<tool id="samtools_sort" name="Sort" version="2.0.1">
+    <description>order of storing aligned sequences</description>
     <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-    <expand macro="stdio"></expand>
-    <expand macro="version_command"></expand>
-    <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        samtools sort
+            $sort_mode
+            -@ \${GALAXY_SLOTS:-1}
+            -o '${output1}'
+            -O bam
+            -T dataset
+            '${input1}'
+    ]]></command>
     <inputs>
         <param name="input1" type="data" format="bam" label="BAM File" />
         <param name="sort_mode" type="select" label="Sort by ">
@@ -29,12 +37,9 @@
         </test>
     </tests>
     <help>
-
 **What it does**
 
 This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
-
-
     </help>
-    <expand macro="citations"></expand>
+    <expand macro="citations"/>
 </tool>