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comparison tophat2_wrapper.xml @ 10:16c4255042be draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit 9f1003eecdf81dc46af598617c8a1042c9d9eb8c
author devteam
date Sun, 01 Jan 2017 07:13:00 -0500
parents 0849fa93eadb
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9:0849fa93eadb 10:16c4255042be
1 <tool id="tophat2" name="TopHat" version="2.1.0"> 1 <tool id="tophat2" name="TopHat" version="2.1.1">
2 <!-- Wrapper compatible with Tophat version 2.0.0+ -->
3 <description>Gapped-read mapper for RNA-seq data</description> 2 <description>Gapped-read mapper for RNA-seq data</description>
4 <macros> 3 <macros>
5 <import>tophat_macros.xml</import> 4 <import>tophat_macros.xml</import>
6 <xml name="paired_parameters"> 5 <xml name="paired_parameters">
7 <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/> 6 <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/>
31 </conditional> 30 </conditional>
32 </actions> 31 </actions>
33 </macro> 32 </macro>
34 </macros> 33 </macros>
35 <requirements> 34 <requirements>
36 <requirement type="package" version="2.2.5">bowtie2</requirement> 35 <requirement type="package" version="2.2.8">bowtie2</requirement>
37 <requirement type="package" version="2.1.0">tophat</requirement> 36 <requirement type="package" version="2.1.1">tophat</requirement>
38 </requirements> 37 </requirements>
39 <stdio> 38 <stdio>
40 <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/> 39 <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
41 <regex match=".*" source="both" level="log" description="tool progress"/> 40 <regex match=".*" source="both" level="log" description="tool progress"/>
42 </stdio> 41 </stdio>