Mercurial > repos > jbrayet > samtools_sort_docker

changeset 5:e95f34f52fc8 draft

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Uploaded
author jbrayet
date Wed, 18 Nov 2015 06:58:13 -0500
parents 6024acc63f80
children b2d324e394ac
files samtools_sort.xml
diffstat 1 files changed, 4 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/samtools_sort.xml	Wed Nov 18 06:57:38 2015 -0500
+++ b/samtools_sort.xml	Wed Nov 18 06:58:13 2015 -0500
@@ -1,11 +1,9 @@
 <tool id="samtools_sort" name="Sort" version="2.0">
     <description>BAM dataset</description>
-    <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-    <expand macro="stdio"></expand>
-    <expand macro="version_command"></expand>
+    <requirements>
+        <requirement type="package" version="0.1">docker_samtools</requirement>
+        <container type="docker">samtools:1.0</container>
+    </requirements>
     <command>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" />
@@ -17,14 +15,10 @@
     <outputs>
         <data name="output1" format="bam" />
     </outputs>
-
     <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>
 </tool>