comparison discosnp_pp.xml @ 4:912d042e4f1e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"

3:297e9d318b48

            ln -sf '${VCF_option.G}' '${reference_file}' &&
        #end if

        run_discoSnp++.sh
        @discosnp_inputs@
        ${t}
        ${T}
        #if str($VCF_option.mapping) == 'reference'
            -G '${reference_file}'
            -M ${VCF_option.M}
            ${VCF_option.R}
        #end if

  ]]></command>

  <inputs>

          <option value="2">No limitation on branching</option>
      </param>

      <expand macro="discosnp_options" />

      <param argument="-t" type="boolean" checked="false" truevalue="-t" falsevalue="" label="Extends each polymorphism with left and right unitigs" />
      <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />

      <conditional name="VCF_option" >
          <param name="mapping" type="select" label="VCF option">
              <option value="default">Do not use reference genome</option>
              <option value="reference">Mapping with a reference genome</option>
          </param>
          <when value="default"></when>
          <when value="reference">
              <param argument="-G" type="data" format="fasta,fastq" label="Reference genome file" />
              <param argument="-M" type="integer" value="4" label="Maximal number of mapping errors" help="during BWA mapping phase" />
              <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" />
          </when>
      </conditional>

  </inputs>

4:912d042e4f1e

            ln -sf '${VCF_option.G}' '${reference_file}' &&
        #end if

        run_discoSnp++.sh
        @discosnp_inputs@
        ${T}
        -b ${b}
        #if str($VCF_option.mapping) == 'reference'
            -G '${reference_file}'
            ${VCF_option.R}
        #end if

        --max_threads \${GALAXY_SLOTS:-1}

  ]]></command>

  <inputs>

          <option value="2">No limitation on branching</option>
      </param>

      <expand macro="discosnp_options" />

      <param argument="-T" type="boolean" checked="false" truevalue="-T" falsevalue="" label="Extends each polymorphism with left and right contigs" />

      <conditional name="VCF_option" >
          <param name="mapping" type="select" label="VCF option">
              <option value="default">Do not use reference genome</option>
              <option value="reference">Mapping with a reference genome</option>
          </param>
          <when value="default"></when>
          <when value="reference">
              <param argument="-G" type="data" format="fasta,fastq" label="Reference genome file" />
              <param argument="-R" type="boolean" truevalue="-R" falsevalue="" checked="false" label="Use the reference genome also in the variant calling, not only for mapping results" />
          </when>
      </conditional>

  </inputs>