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

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/tophat2 commit 9f1003eecdf81dc46af598617c8a1042c9d9eb8c

9:0849fa93eadb

<tool id="tophat2" name="TopHat" version="2.1.0">
    <!-- Wrapper compatible with Tophat version 2.0.0+ -->
    <description>Gapped-read mapper for RNA-seq data</description>
    <macros>
      <import>tophat_macros.xml</import>
      <xml name="paired_parameters">
        <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."/>

          </conditional>
        </actions>
      </macro>
    </macros>
    <requirements>
        <requirement type="package" version="2.2.5">bowtie2</requirement>
        <requirement type="package" version="2.1.0">tophat</requirement>
    </requirements>
    <stdio>
        <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

10:16c4255042be

<tool id="tophat2" name="TopHat" version="2.1.1">
    <description>Gapped-read mapper for RNA-seq data</description>
    <macros>
      <import>tophat_macros.xml</import>
      <xml name="paired_parameters">
        <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."/>

          </conditional>
        </actions>
      </macro>
    </macros>
    <requirements>
        <requirement type="package" version="2.2.8">bowtie2</requirement>
        <requirement type="package" version="2.1.1">tophat</requirement>
    </requirements>
    <stdio>
        <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>