annotate tophat_macros.xml @ 1:6eaefb5f755a

Update Tophat URLs in help text.

<macros>
  <macro name="refGenomeSourceConditional">
    <conditional name="refGenomeSource">
      <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
        <option value="indexed" selected="True">Use a built-in genome</option>
        <option value="history">Use a genome from history</option>
      </param>
      <when value="indexed">
        <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
          <yield />
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
      </when>  <!-- history -->
    </conditional>  <!-- refGenomeSource -->
  </macro>
  <macro name="indel_searchConditional">
    <conditional name="indel_search">
      <param name="allow_indel_search" type="select" label="Allow indel search">
        <option value="Yes">Yes</option>
        <option value="No">No</option>
      </param>
      <when value="No"/>
      <when value="Yes">
        <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
        <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
      </when>
    </conditional>    
  </macro>
  <macro name="own_junctionsConditional">
    <conditional name="own_junctions">
      <param name="use_junctions" type="select" label="Use Own Junctions">
        <option value="No">No</option>
        <option value="Yes">Yes</option>
      </param>
      <when value="Yes">
        <conditional name="gene_model_ann">
          <param name="use_annotations" type="select" label="Use Gene Annotation Model">
            <option value="No">No</option>
            <option value="Yes">Yes</option>
          </param>
          <when value="No" />
          <when value="Yes">
            <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
          </when>
        </conditional>
        <expand macro="raw_juncsConditional" />
        <expand macro="no_novel_juncsParam" />
      </when>
      <when value="No" />
    </conditional> <!-- /own_junctions -->
  </macro>
  <macro name="raw_juncsConditional">
    <conditional name="raw_juncs">
      <param name="use_juncs" type="select" label="Use Raw Junctions">
        <option value="No">No</option>
        <option value="Yes">Yes</option>
      </param>
      <when value="No" />
      <when value="Yes">
        <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
      </when>
    </conditional>
  </macro>
  <macro name="no_novel_juncsParam">
    <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
      <option value="No">No</option>
      <option value="Yes">Yes</option>
    </param>
  </macro>    
</macros>