Galaxy tool descriptor for maf_tile

maf_tile.xml

<tool id="bio_maf_tile" name="Tile MAF blocks with reference sequence"
      version="1.0.1">
    <description>Concatenates multiple alignments for a set of
    intervals, filling gaps from a reference sequence</description>
    <command interpreter="bash">
        bioruby_runner maf_tile --bed $input1
        #if $bed_species:
        --bed-species $bed_species
        #end if
        #if $one_based then "--one-based" else ""#
        #if $maf_source_type.species:
        --species $maf_source_type.species
        #else
        --species-file $species_map
        #end if
        #if $ref_seq:
        --reference $ref_seq
        #end if
        --concat
        --output-base $out_file1
        --fill-char '$fill_char'
        #if $upcase then "--upcase" else ""#
        $maf_file
    </command>
    <!--
        galaxy.tools WARNING 2012-08-17 17:22:35,640 Invalid range start for tool's exit_code : exit_code ignored
    -->
    <!--
    <stdio>
        <exit_code value="0" />
    </stdio>
    -->
    <inputs>
        <page>
            <param name="input1" type="data" format="bed" label="BED file">
                <validator type="unspecified_build" />
            </param>
            <param name="bed_species" type="text" 
                   label="Species prefix" />
            <param name="one_based" type="boolean" optional="false"
                   label="Treat BED intervals as one-based (nonstandard)?"
                   value="false" />

            <conditional name="maf_source_type">
                <param name="maf_source" type="select" label="MAF Source">
                    <option value="cached" selected="true">Locally Cached Alignments</option>
                    <option value="user">Alignments in Your History</option>
                </param>
                <when value="user">
                    <param name="maf_file" type="data" format="maf" label="MAF File">
                        <options>
                            <filter type="data_meta" ref="input1" key="dbkey" />
                        </options>
                        <validator type="dataset_ok_validator" />
                    </param>
                    <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
                        <options>
                            <filter type="data_meta" ref="maf_file" key="species" />
                        </options>
                    </param>
                </when>
                <when value="cached">
                    <param name="maf_identifier" type="select" label="MAF Type" >
                        <options from_file="maf_index.loc">
                            <column name="name" index="0"/>
                            <column name="value" index="1"/>
                            <column name="dbkey" index="2"/>
                            <column name="species" index="3"/>
                            <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>
                            <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
                        </options>
                    </param> 
                    <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
                        <options from_file="maf_index.loc">
                            <column name="uid" index="1"/>
                            <column name="value" index="3"/>
                            <column name="name" index="3"/>
                            <filter type="param_value" ref="maf_identifier" name="uid" column="1"/>
                            <filter type="multiple_splitter" column="3" separator=","/>
                        </options>
                    </param>
                </when>
            </conditional>
            <param name="ref_seq" type="data" format="fasta"
                   optional="true" label="FASTA reference sequence">
                <help>
                    Optional FASTA reference sequence for chromosome
                    being used. Will be used to fill in gaps.
                </help>
            </param>
            <param name="species_map" type="data" format="txt"
                   optional="true" label="Species mapping file">
                <help>
                    Optional text file listing species to extract (if
                    none are selected with checkboxes above) and
                    optional output names to map them to. Each line is
                    a species entry; it may be followed by whitespace
                    and an output name.
                </help>
            </param>
            <param name="upcase" type="boolean" optional="false"
                   label="Fold sequence data to upper case?"
                   value="false" />
            <param name="fill_char" type="text" size="1"
                   optional="false"
                   value="*"
                   label="Fill gaps with character" />
        </page>
    </inputs>
    <outputs>
        <data format="fasta" name="out_file1" />
    </outputs>
    <requirements>
        <requirement type="binary">maf_tile</requirement>
    </requirements>
    <help>
        This tool will synthesize a multiple alignment for a set of
        genomic intervals (exons, for instance) given by a BED
        file. Any parts of these intervals not covered by alignments
        in the chosen MAF file will be filled in from a FASTA
        reference sequence. The output will be a single alignment
        block in FASTA format.
    </help>
</tool>