comparison translate_bed_sequences.xml @ 3:3b526a780849

Change default seqtype from pep:novel to pep:splice

2:359addb9b9d4

    <param name="input" type="data" format="bed" label="BED file with added sequence column" 
           help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> 
    <param name="reference" type="text" value="" optional="true" label="Genome reference name"
           help="By default, the database metadata will be used."/>
    <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
           help="For example:  pep:novel"/>
    <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
           help="For example:  with the tag name 'depth' and bed score 12:   depth:12"/>
    <conditional name="filter">
      <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">
        <option value="yes" selected="true">Yes</option>

3:3b526a780849

    <param name="input" type="data" format="bed" label="BED file with added sequence column" 
           help="Output from 'Extract Genomic DNA' run on tophat junctions.bed "/> 
    <param name="reference" type="text" value="" optional="true" label="Genome reference name"
           help="By default, the database metadata will be used."/>
    <param name="seqtype" type="text" value="" optional="true" label="The SEQTYPE:STATUS to include in the fasta ID lines"
           help="For example:  pep:splice"/>
    <param name="score_name" type="text" value="" optional="true" label="Add the bed score field fasta ID line with this tag name"
           help="For example:  with the tag name 'depth' and bed score 12:   depth:12"/>
    <conditional name="filter">
      <param name="filterseqs" type="select" label="Filter out translations with stop codons before the splice site">
        <option value="yes" selected="true">Yes</option>