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changeset 23:74aebe30fb52 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 67da1a478db26ad45f36a673218d526f8962d72f"
author iuc
date Sun, 19 Jan 2020 09:43:43 -0500
parents 268d162b9c49
children cfcf33df7fc0
files snpEff_macros.xml snpeff_get_chr_names.xml
diffstat 2 files changed, 6 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/snpEff_macros.xml	Fri Oct 18 06:12:18 2019 -0400
+++ b/snpEff_macros.xml	Sun Jan 19 09:43:43 2020 -0500
@@ -1,6 +1,7 @@
 <macros>
     <xml name="requirement">
         <requirement type="package" version="4.3.1t">snpeff</requirement>
+        <yield/>
     </xml>
   <xml name="stdio">
     <stdio>
--- a/snpeff_get_chr_names.xml	Fri Oct 18 06:12:18 2019 -0400
+++ b/snpeff_get_chr_names.xml	Sun Jan 19 09:43:43 2020 -0500
@@ -1,14 +1,16 @@
-<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@WRAPPER_VERSION@.galaxy1">
+<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@WRAPPER_VERSION@.galaxy2">
     <description>list chromosome names/lengths</description>
     <macros>
         <import>snpEff_macros.xml</import>
     </macros>
     <requirements>
-        <expand macro="requirement" />
+        <expand macro="requirement">
+            <requirement type="package" version="5.0.1">gawk</requirement>
+        </expand>
     </requirements>
     <expand macro="stdio" />
     <expand macro="version_command" />
-    <command><![CDATA[
+    <command detect_errors="exit_code"><![CDATA[
       snpEff @JAVA_OPTIONS@ dump
       #if $snpDb.genomeSrc == 'cached':
         -dataDir ${snpDb.genomeVersion.fields.path}