comparison snp_caller_caller.xml @ 4:ffee8534a5c4

upgrade to mimodd version 0.1.6

3:ba685c655e18

  <inputs>
    <param name="ref_genome" type="data" format="fasta" label="reference genome" />
    <repeat name="list_input" title="Aligned reads input source" default="1" min="1">
      <param name="inputfile" type="data" format="bam" label="input file" />
    </repeat>
    <param name="group_by_id" type="boolean" label="group reads based on read group id only" truevalue="-i" falsevalue="" checked="true" help="If selected, this option ensures that only the read group id (but not the sample name) is considered in grouping reads in the input file(s). If turned off, read groups with identical sample names are automatically pooled and analyzed together even if they come from different NGS runs." />
    <param name="no_md5_check" type="boolean" label="turn off md5 sum verification" truevalue="-x" falsevalue="" checked="false" help="leave turned on to avoid accidental variant calling against a wrong reference genome version (see the tool help below)." />
    <param name="depth" type="integer" value="250" label="maximum per-BAM depth (default: 250)" help="to avoid excessive use of memory"/>
  </inputs>

  <outputs>

4:ffee8534a5c4

  <inputs>
    <param name="ref_genome" type="data" format="fasta" label="reference genome" />
    <repeat name="list_input" title="Aligned reads input source" default="1" min="1">
      <param name="inputfile" type="data" format="bam" label="input file" />
    </repeat>
    <param name="group_by_id" type="boolean" label="group reads based on read group id only" truevalue="-i" falsevalue="" checked="false" help="If selected, this option ensures that only the read group id (but not the sample name) is considered in grouping reads in the input file(s). If turned off, read groups with identical sample names are automatically pooled and analyzed together even if they come from different NGS runs." />
    <param name="no_md5_check" type="boolean" label="turn off md5 sum verification" truevalue="-x" falsevalue="" checked="false" help="leave turned on to avoid accidental variant calling against a wrong reference genome version (see the tool help below)." />
    <param name="depth" type="integer" value="250" label="maximum per-BAM depth (default: 250)" help="to avoid excessive use of memory"/>
  </inputs>

  <outputs>