comparison vcf_to_alignment.xml @ 1:4b9ddf64558d draft

planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit c467fa511c437e11ea72b912975d64631b8d0f98

0:cc255feec53b

    #end for
    --reference_file
    #if str($reference.source) == 'history':
      reference.fasta
    #else
      '${reference.builtin}'
    #end if
    --output_file '${output_alignment}'
    ]]>
  </command>
  <inputs>

        <param name="history" type="data" format="fasta" label="Reference sequence" />
      </when>
      <when value="builtin">
        <param name="builtin" type="select" label="Reference sequence (FASTA format)">
          <options from_data_table="all_fasta" />
        </param>
      </when>
    </conditional>
  </inputs>
  <outputs>

1:4b9ddf64558d

    #end for
    --reference_file
    #if str($reference.source) == 'history':
      reference.fasta
    #else
      '${reference.builtin.fields.path}'
    #end if
    --output_file '${output_alignment}'
    ]]>
  </command>
  <inputs>

        <param name="history" type="data" format="fasta" label="Reference sequence" />
      </when>
      <when value="builtin">
        <param name="builtin" type="select" label="Reference sequence (FASTA format)">
          <options from_data_table="all_fasta" />
          <validator type="no_options" message="No FASTA datasets are available for the selected input dataset" />
        </param>
      </when>
    </conditional>
  </inputs>
  <outputs>