galaxy/tools/sr_mapping/bowtie2_wrapper.xml

<tool id="bowtie2" name="Bowtie2" version="0.1">
    <!-- Wrapper compatible with Bowtie version 2.0.0 -->
    <description>is a short-read mapper</description>
    <version_command>bowtie2 --version</version_command>
    <requirements>
        <requirement type="package">bowtie2</requirement>
    </requirements>
    <command interpreter="python">
        bowtie2_wrapper.py
        
        ## Change this to accommodate the number of threads you have available.
        --num-threads="4"

        ## Outputs.
        --output=$output

        ## Handle reference file.
        #if $refGenomeSource.genomeSource == "history":
            --own-file=$refGenomeSource.ownFile
        #else:
            --indexes-path="${refGenomeSource.index.fields.path}"
        #end if

        ## Are reads single-end or paired?
        --single-paired=$singlePaired.sPaired

        ## First input file always required.
        --input1=$input1
        
        ## Second input only if input is paired-end.
        #if $singlePaired.sPaired == "paired"
            --input2=$singlePaired.input2
            -I $singlePaired.minInsert
            -X $singlePaired.maxInsert
        #end if

        ## Set params.
        --settings=$params.settingsType
        
        #if $params.settingsType == "full":
            #if str($params.align_type) == "end_to_end":
                --end-to-end --preset-alignment=$params.preset.align_preset_select
            #else:
                --local --preset-alignment=$params.preset.align_preset_select-local
            #end if
        #end if
    </command>
    <inputs>
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Is this library mate-paired?">
              <option value="single">Single-end</option>
              <option value="paired">Paired-end</option>
            </param>
            <when value="single">
                <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
            </when>
            <when value="paired">
                <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                <param format="fastqsanger" name="input2" type="data" label="FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                <!-- TODO: paired-end specific parameters. -->
                <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
                <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
            </when>
        </conditional>
        <conditional name="refGenomeSource">
          <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
            <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 the Galaxy team">
              <options from_data_table="bowtie2_indexes">
                <filter type="sort_by" column="2"/>
                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
              </options>
            </param>
          </when>
          <when value="history">
            <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
          </when>  <!-- history -->
        </conditional>  <!-- refGenomeSource -->
        <conditional name="params">
            <param name="settingsType" type="select" label="Bowtie settings to use" help="You can use the default settings or set custom values for any of Bowtie's parameters.">
              <option value="preSet">Use Defaults</option>
              <option value="full">Full parameter list</option>
            </param>
            <when value="preSet" />
            <!-- Full/advanced params. -->
            <when value="full">
                <param name="align_type" type="select" label="Type of alignment">
                    <option selected="true" value="end_to_end">End to end</option>
                    <option value="local">Local</option>
                </param>
                <conditional name="preset">
                    <param name="b2_preset" type="select" label="Use Preset options">
                          <option selected="true" value="Yes">Yes</option>
                          <option value="No">No</option>
                    </param>
                    <when value="Yes">
                        <param name="align_preset_select" type="select" label="Preset option">
                            <option value="very-fast">Very fast</option>
                            <option value="fast">Fast</option>
                            <option selected="true" value="sensitive">Sensitive</option>
                            <option value="very-sensitive">Very sensitive</option>
                        </param>
                    </when>
                    <!-- TODO: -->
                    <when value="No" />
                </conditional>
            </when>  <!-- full -->
      </conditional>  <!-- params -->
    </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="bowtie2_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>
              <when value="history">
                <action type="metadata" name="dbkey">
                  <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
                </action>
              </when>
            </conditional>
          </actions>
        </data>
    </outputs>

    <tests>
    </tests>

    <help>
    </help>
</tool>