comparison rsem_prepare_reference.xml @ 3:59459de65740

mv RSEM datatypes to separate repository, remove samtools dependency

2:5949673f9e3e

  <requirements>
    <requirement type="package" version="1.1.17">rsem</requirement>
    <requirement type="package" version="1.0.0">bowtie</requirement>
  </requirements>
  <command>
    mkdir $reference_file.extra_files_path &amp;&amp; 
    cd $reference_file.extra_files_path &amp;&amp; 
    rsem-prepare-reference 
    #if $polya.polya_use == 'add':
      #if $polya.polya_length:

    #else:
      --gtf $reference.gtf
      $reference.reference_fasta_file
    #end if
    $reference_name
  </command>
  <inputs>
    <conditional name="reference">
      <param name="ref_type" type="select" label="Reference transcript source">
        <option value="transcripts">transcript fasta</option>

          If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file. 
          Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
      </help>
    </param>
    <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
      <help>A one work name for this RSEM reference containing only letters, digits, and underscore characters</help>
      <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
    </param>
    <conditional name="polya">
      <param name="polya_use" type="select" label="PolyA ">
        <option value="add" selected="true">Add poly(A) tails to all transcripts</option>

3:59459de65740

  <requirements>
    <requirement type="package" version="1.1.17">rsem</requirement>
    <requirement type="package" version="1.0.0">bowtie</requirement>
  </requirements>
  <command>
    echo $reference_name " " | tee $reference_file &amp;&amp;
    mkdir $reference_file.extra_files_path &amp;&amp; 
    cd $reference_file.extra_files_path &amp;&amp; 
    rsem-prepare-reference 
    #if $polya.polya_use == 'add':
      #if $polya.polya_length:

    #else:
      --gtf $reference.gtf
      $reference.reference_fasta_file
    #end if
    $reference_name
    > ${reference_name}.log
  </command>
  <inputs>
    <conditional name="reference">
      <param name="ref_type" type="select" label="Reference transcript source">
        <option value="transcripts">transcript fasta</option>

          If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file. 
          Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
      </help>
    </param>
    <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
      <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help>
      <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
    </param>
    <conditional name="polya">
      <param name="polya_use" type="select" label="PolyA ">
        <option value="add" selected="true">Add poly(A) tails to all transcripts</option>