comparison bowtie_wrapper.xml @ 7:2c811e06006a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers commit 397bc85634156862fdaa3d74b8f1e53752876619

6:ecbbc8be6266

<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.2.0">
  <requirements>
    <requirement type="package" version="1.2.0">bowtie</requirement>
  </requirements>
  <description></description>
  <version_command>bowtie --version</version_command>
  <command>
    python '$__tool_directory__/bowtie_wrapper.py'
      ## Set number of threads
      --threads="\${GALAXY_SLOTS:-4}"

            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="bowtie_base_index,fasta" metadata_name="dbkey" label="Select the reference genome" />
        <conditional name="indexParams">
          <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index">
            <option value="indexPreSet">Default</option>
            <option value="indexFull">Set your own</option>
          </param>

        </conditional> <!-- sParams -->
      </when> <!-- single -->
      <when value="paired">
        <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
        <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
            <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">>
               <column name="name" index="0"/>
               <column name="value" index="0"/>
               <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
           </options>
        </param>

7:2c811e06006a

<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.2.0">
  <description></description>
  <requirements>
    <requirement type="package" version="1.2.0">bowtie</requirement>
  </requirements>
  <version_command>bowtie --version</version_command>
  <command>
    python '$__tool_directory__/bowtie_wrapper.py'
      ## Set number of threads
      --threads="\${GALAXY_SLOTS:-4}"

            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="bowtie_base_index,fasta" label="Select the reference genome" />
        <conditional name="indexParams">
          <param name="indexSettings" type="select" label="Choose whether to use Default options for building indices or to Set your own" help="These settings are ignored when using a prebuilt index">
            <option value="indexPreSet">Default</option>
            <option value="indexFull">Set your own</option>
          </param>

        </conditional> <!-- sParams -->
      </when> <!-- single -->
      <when value="paired">
        <param name="pInput1" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
        <param name="pInput2" type="data" format="fastqsanger,fastqillumina,fastqsolexa" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file">
            <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
               <column name="name" index="0"/>
               <column name="value" index="0"/>
               <filter type="param_value" ref="pInput1" ref_attribute="ext" column="0"/>
           </options>
        </param>