Mercurial > repos > simon-gladman > snippy

changeset 10:0c9f91faff96 draft

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Added zippeed output folder as an output for use in snippy core.
author simon-gladman
date Wed, 08 Jun 2016 09:56:14 -0400
parents 234020dc16f7
children 68a43b0593a3
files snippy.xml tool_dependencies.xml
diffstat 2 files changed, 7 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/snippy.xml	Wed Jun 08 02:56:35 2016 -0400
+++ b/snippy.xml	Wed Jun 08 09:56:14 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="snippy" name="snippy" version="0.3">
+<tool id="snippy" name="snippy" version="0.2.0">
     <requirements>
       <requirement type="package" version="3.0">snippy</requirement>
     </requirements>
@@ -53,6 +53,10 @@
 
       gunzip out/snps.depth.gz
 
+      &&
+
+      bgzip -c out > out.bgz
+
 
     ]]></command>
     <inputs>
@@ -119,6 +123,7 @@
       <data format="bam" name="snpsbam" label="${tool.name} on ${on_string} mapped reads (bam)" from_work_dir="out/snps.bam">
         <filter>cleanup is False</filter>
       </data>
+      <data format="bgzip" name="outdir" label="${tool.name} on ${on_string} out dir" from_work_dir="out.bgz" />
     </outputs>
 
     <tests>
--- a/tool_dependencies.xml	Wed Jun 08 02:56:35 2016 -0400
+++ b/tool_dependencies.xml	Wed Jun 08 09:56:14 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="snippy" version="3.0">
-        <repository changeset_revision="eb1762cb97e5" name="package_snippy_3_0" owner="simon-gladman" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="f94a38e62a98" name="package_snippy_3_0" owner="simon-gladman" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>