comparison snippy.xml @ 11:68a43b0593a3 draft

Updated to new version of snippy with static binaries

10:0c9f91faff96

<tool id="snippy" name="snippy" version="0.2.0">
    <requirements>
      <requirement type="package" version="3.0">snippy</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command><![CDATA[
      #if str( $reftype.ref_type_selector ) == "fasta"
        cp $reftype.ref foo.fna &&
      #end if

      gunzip out/snps.depth.gz

      &&

      bgzip -c out > out.bgz


    ]]></command>
    <inputs>
      <conditional name="reftype">

  --rgid [X]        Use this @RG ID: in the BAM header (default '')

  --bwaopt [X]      Extra BWA MEM options, eg. -x pacbio (default '')

    ]]></help>

    <citations>
      <citation type="bibtex">@UNPUBLISHED{Seemann2013,
        author = "Seemann T",
        title = "snippy: fast bacterial variant calling from NGS reads",
        year = "2015",
        note = "https://github.com/tseemann/snippy"}
      </citation>
    </citations>

</tool>

11:68a43b0593a3

<tool id="snippy" name="snippy" version="0.2.0">
  <macros>
      <import>macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="stdio" />

    <command><![CDATA[
      #if str( $reftype.ref_type_selector ) == "fasta"
        cp $reftype.ref foo.fna &&
      #end if

      gunzip out/snps.depth.gz

      &&

      gzip -cr out > out.gz


    ]]></command>
    <inputs>
      <conditional name="reftype">

  --rgid [X]        Use this @RG ID: in the BAM header (default '')

  --bwaopt [X]      Extra BWA MEM options, eg. -x pacbio (default '')

    ]]></help>
    <expand macro="citations" />


</tool>