comparison shapeit_phase.xml @ 18:d3515c2a3f51 draft

planemo upload for repository https://github.com/CPGRZA/cpgr_ancestry commit 40d1319d78fae41b53fe3511db41ee5479c58db8-dirty

17:1f460ad509b6

<tool id="shapeit_phase" name="shapeit_phase" version="0.16.0">
    <description>genomic data with or without reference panel</description>
    <requirements>
        <requirement type="package" version="2.r837">shapeit</requirement>
    </requirements>
    <stdio>

          --output-max $out_haps $out_sample
          --output-graph $out_graph
          --output-log $out_log
        #else
          --output-log output
          | grep -v 'ERROR: Reference and Main panels are not well aligned:'
          ; mv output.mendel.log $out_log
          && mv output.mendel.snp.strand $out_strand
          && mv output.mendel.snp.strand.exclude $out_exclude
        #end if
        # NOTE that in check mode we are ignoring the error related to panel misalignment
    ]]></command>
    <inputs>
      <param name="check_mode" type="boolean" truevalue="-check" falsevalue="" label="Run in -check mode (check data)" />

18:d3515c2a3f51

<tool id="shapeit_phase" name="shapeit_phase" version="0.17.0">
    <description>genomic data with or without reference panel</description>
    <requirements>
        <requirement type="package" version="2.r837">shapeit</requirement>
    </requirements>
    <stdio>

          --output-max $out_haps $out_sample
          --output-graph $out_graph
          --output-log $out_log
        #else
          --output-log output
          | grep -v 'ERROR:.* Reference and Main panels are not well aligned:'
          ; mv output.log $out_log
          && mv output.snp.strand $out_strand
          && mv output.snp.strand.exclude $out_exclude
        #end if
        # NOTE that in check mode we are ignoring the error related to panel misalignment
    ]]></command>
    <inputs>
      <param name="check_mode" type="boolean" truevalue="-check" falsevalue="" label="Run in -check mode (check data)" />