comparison bowtie_transcriptome_wrapper/bowtie_transcriptomic_wrapper.xml @ 19:75f8e498d26f draft

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18:5fe541e5198b

<tool id="bowtie_transcriptomic_wrapper" name="Bowtie Transcriptome Alignment" version="1.7.4">
  <description>Align to Transcriptome using 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" help="if your reference of interest is not listed - contact RiboGalaxy team">
          <options from_data_table="bowtie_transcriptome_indexes">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>

    <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_transcriptome_indexes" column="1" offset="0">
                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
              </option>
            </action>
          </when>

19:75f8e498d26f

<tool id="bowtie_trans_wrapper" name="Bowtie Transcriptome Alignment" version="1.7.5">
  <description>Align to Transcriptome using 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" help="if your reference of interest is not listed - contact RiboGalaxy team">
          <options from_data_table="bowtie_transcriptome_indexes_3">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>

    <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_transcriptome_indexes_3" column="1" offset="0">
                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                <filter type="param_value" ref="refGenomeSource.index" column="0"/>
              </option>
            </action>
          </when>