annotate velvet_macro.xml @ 2:1bb80c25b379 draft

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<macros>

  <xml name="paired_library_options">
    <param name="ins_length" type="integer" optional="true" label="Expected distance between two paired end reads"/>
    <param name="ins_length_sd" type="integer" optional="true" label="Standard deviation for paired end reads length (default: 10% of corresponding length)"/>
    <repeat min="1" name="files" title="Input files">
      <conditional name="fileFormat">
        <param name="format" type="select" label="File format">
          <option value="-fasta">fasta</option>
          <option value="-fastq">fastq</option>
          <option value="-fasta_gz">fasta.gz</option>
          <option value="-fastq_gz">fastq.gz</option>
        </param>
        <when value="-fasta">
          <conditional name="fileLayout">
            <param name="layout" type="select" label="File layout">
              <option value="-interleaved">interleaved</option>
              <option value="-separate">separate</option>
            </param>
            <when value="-interleaved">
              <param name="sequence" type="data" format="fasta" label="Interleaved sequence file"/>
            </when>
            <when value="-separate">
              <param name="sequence" type="data" format="fasta" label="Forward sequence file"/>
              <param name="sequencePair" type="data" format="fasta" optional="true" label="Reverse sequence file"/>
            </when>
          </conditional>
        </when>
        <when value="-fasta_gz">
          <conditional name="fileLayout">
            <param name="layout" type="select" label="File layout">
              <option value="-interleaved">interleaved</option>
              <option value="-separate">separate</option>
            </param>
            <when value="-interleaved">
              <param name="sequence" type="data" format="fasta.gz" label="Interleaved sequence file"/>
            </when>
            <when value="-separate">
              <param name="sequence" type="data" format="fasta.gz" label="Forward sequence file"/>
              <param name="sequencePair" type="data" format="fasta.gz" optional="true" label="Reverse sequence file"/>
            </when>
          </conditional>
        </when>
        <when value="-fastq">
          <conditional name="fileLayout">
            <param name="layout" type="select" label="File layout">
              <option value="-interleaved">interleaved</option>
              <option value="-separate">separate</option>
            </param>
            <when value="-interleaved">
              <param name="sequence" type="data" format="fastq" label="Interleaved sequence file"/>
            </when>
            <when value="-separate">
              <param name="sequence" type="data" format="fastq" label="Forward sequence file"/>
              <param name="sequencePair" type="data" format="fastq" optional="true" label="Reverse sequence file"/>
            </when>
          </conditional>
        </when>
        <when value="-fastq_gz">
          <conditional name="fileLayout">
            <param name="layout" type="select" label="File layout">
              <option value="-interleaved">interleaved</option>
              <option value="-separate">separate</option>
            </param>
            <when value="-interleaved">
              <param name="sequence" type="data" format="fastq.gz" label="Interleaved sequence file"/>
            </when>
            <when value="-separate">
              <param name="sequence" type="data" format="fastq.gz" label="Forward sequence file"/>
              <param name="sequencePair" type="data" format="fastq.gz" optional="true" label="Reverse sequence file"/>
            </when>
          </conditional>
        </when>
      </conditional>
    </repeat>
  </xml>

  <token name="@PAIRED_FILES_OPTIONS@">

    #for $j, $file in enumerate( $library.files )

      $file.fileFormat.format

      #if $file.fileFormat.fileLayout.layout == "-separate"
        -separate $file.fileFormat.fileLayout.sequence $file.fileFormat.fileLayout.sequencePair
      #else
        -interleaved $file.fileFormat.fileLayout.sequence
      #end if

    #end for

  </token>

  <xml name="unpaired_library_options">
    <repeat min="1" name="files" title="Input files">
      <conditional name="fileFormat">
        <param name="format" type="select" label="File format">
          <option value="-fasta">fasta</option>
          <option value="-fastq">fastq</option>
          <option value="-raw">raw</option>
          <option value="-fasta_gz">fasta.gz</option>
          <option value="-fastq_gz">fastq.gz</option>
          <option value="-raw_gz">raw.gz</option>
          <option value="-sam">sam</option>
          <option value="-bam">bam</option>
        </param>
        <when value="-fasta">
          <param name="sequence" type="data" format="fasta" label="Sequence file"/>
        </when>
        <when value="-fasta_gz">
          <param name="sequence" type="data" format="fasta.gz" label="Sequence file"/>
        </when>
        <when value="-fastq">
          <param name="sequence" type="data" format="fastq" label="Sequence file"/>
        </when>
        <when value="-fastq_gz">
          <param name="sequence" type="data" format="fastq.gz" label="Sequence file"/>
        </when>
        <when value="-raw">
          <param name="sequence" type="data" format="txt" label="Sequence file"/>
        </when>
        <when value="-raw_gz">
          <param name="sequence" type="data" format="txt" label="Sequence file"/>
        </when>
        <when value="-sam">
          <param name="sequence" type="data" format="sam" label="Sequence file"/>
        </when>
        <when value="-bam">
          <param name="sequence" type="data" format="bam" label="Sequence file"/>
        </when>
      </conditional>
    </repeat>
  </xml>

  <token name="@UNPAIRED_FILES_OPTIONS@">

    #for $j, $file in enumerate( $library.files )

      $file.fileFormat.format

      $file.fileFormat.sequence

    #end for

  </token>

</macros>