view data_manager/macros.xml @ 1:6127cd38980b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 056ae20332ed001ad50a7e733df3595108172c6c-dirty

<macros>
    <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
    whenever you make changes to the following two version tokens!
    The data manager uses a symlink to this macro file to keep the versions in
    sync. -->
    <!-- STAR version to be used -->
    <token name="@VERSION@">2.7.1a</token>
    <!-- STAR index version compatible with this version of STAR
    This is the STAR version that introduced the index structure expected
    by the current version.
    It can be found for any specific version of STAR with:
    STAR -h | grep versionGenome
    or by looking for the versionGenome parameter in source/parametersDefault
    of STAR's source code -->
    <token name="@IDX_VERSION@">2.7.1a</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">star</requirement>
            <requirement type="package" version="1.9">samtools</requirement>
        </requirements>
    </xml>

    <xml name="index_selection" token_with_gene_model="1">
        <param argument="--genomeDir" name="genomeDir" type="select"
        label="Select reference genome"
        help="If your genome of interest is not listed, contact the Galaxy team">
            <options from_data_table="rnastar_index2_versioned">
                <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
                <filter type="static_value" column="5" value="@IDX_VERSION@" />
                <filter type="sort_by" column="2" />
                <validator type="no_options" message="No indexes are available for the selected input dataset" />
            </options>
        </param>
    </xml>

    <token name="@FASTQ_GZ_OPTION@">
        --readFilesCommand zcat
    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/bioinformatics/bts635</citation>
        </citations>
    </xml>
    <xml name="@SJDBOPTIONS@" token_optional="true">
         <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
         <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
    </xml>
    <xml name="dbKeyActions">
        <actions>
            <conditional name="refGenomeSource.geneSource">
                <when value="indexed">
                    <action type="metadata" name="dbkey">
                        <option type="from_data_table" name="rnastar_index2_versioned" column="1" offset="0">
                            <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                            <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
                        </option>
                    </action>
                </when>
                <when value="history">
                    <action type="metadata" name="dbkey">
                        <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
                    </action>
                </when>
            </conditional>
        </actions>
    </xml>
</macros>