comparison bowtie_genome_wrapper/bowtie_genomic_wrapper.xml @ 14:a1565147cdc8 draft default tip

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13:e8551e16829c

<tool id="bowtie_genomic_wrapper" name="Bowtie Genome Alignment" version="1.6.0">
  <description>Align to the Genome with Bowtie</description>
  <requirements>
    <requirement type="package" version="1.2.0">bowtie</requirement>
    <requirement type="package" version="1.13">samtools</requirement>

        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the 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 Galaxy team">
          <options from_data_table="bowtie_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>

    </conditional> <!-- singlePaired -->
    <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
    <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
  </inputs>
  <outputs>
    <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
      <actions>
        <conditional name="refGenomeSource.genomeSource">
          <when value="indexed">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">

14:a1565147cdc8

<tool id="bowtie_genomic_wrapper" name="Bowtie Genome Alignment" version="1.7.1">
  <description>Align to the Genome with Bowtie</description>
  <requirements>
    <requirement type="package" version="1.2.0">bowtie</requirement>
    <requirement type="package" version="1.13">samtools</requirement>

        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the 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 Galaxy team">
          <options from_data_table="bowtie_genome_refs2">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>

    </conditional> <!-- singlePaired -->
    <param name="save_mapping_stats" type="boolean" checked="False" label="Save the bowtie mapping statistics to the history" />
    <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file (--sam-nohead)" help="Bowtie produces SAM with several lines of header information by default" />
  </inputs>
  <outputs>
    <data format="bam" name="output" label="${tool.name} on ${on_string}: mapped reads">
      <actions>
        <conditional name="refGenomeSource.genomeSource">
          <when value="indexed">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="bowtie_indexes" column="1" offset="0">