comparison cufflinks_wrapper.xml @ 3:3afd198a1cf0 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cufflinks commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5

2:a6f581469476

<tool id="cufflinks" name="Cufflinks" version="@VERSION@.1">
    <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <requirements>
      <requirement type="package" version="0.7.3">bx-python</requirement>
      <requirement type="package" version="1.9.0">six</requirement>
      <requirement type="package" version="2.2.1">cufflinks</requirement>
    </requirements>
    <expand macro="stdio" />
    <version_command>cufflinks 2>&amp;1 | head -n 1</version_command>
    <command>
        python '$__tool_directory__/cufflinks_wrapper.py'
            --input '$input'
            --assembled-isoforms-output '$assembled_isoforms'
            --num-threads "\${GALAXY_SLOTS:-4}"
            -I $max_intron_len

3:3afd198a1cf0

<tool id="cufflinks" name="Cufflinks" version="@VERSION@.2">
    <description>transcript assembly and FPKM (RPKM) estimates for RNA-Seq data</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>cufflinks 2>&amp;1 | head -n 1</version_command>
    <command detect_errors="aggressive">
        python '$__tool_directory__/cufflinks_wrapper.py'
            --input '$input'
            --assembled-isoforms-output '$assembled_isoforms'
            --num-threads "\${GALAXY_SLOTS:-4}"
            -I $max_intron_len