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<tool id="tophat_fusion_post" name="Tophat Fusion Post" version="0.1">
    <description>post-processing to identify fusion genes</description>
    <version_command>tophat-fusion-post --version</version_command>
    <requirements>
        <requirement type="package">tophat2</requirement>
    </requirements>
    <command>
        ## Set up tophat_out structure.
        mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out;

        ## Set up blast directory structure.
        #set blast_db_path = ${__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
        ln -s ${blast_db_path}/ blast;

        ## Set up additional files:
	    ln -s ${blast_db_path}/refGene.txt .;
	    ln -s ${blast_db_path}/ensGene.txt .;
        ln -s ${blast_db_path}/mcl .;

        ## Run tophat-fusion-post
        tophat-fusion-post -p 22
        --num-fusion-reads $num_fusion_reads --num-fusion-pairs $num_fusion_pairs --num-fusion-both $num_fusion_both --fusion-read-mismatches $fusion_read_mismatches --fusion-multireads $fusion_multireads
        #if str($is_human) == 'No':
              --non-human
        #end if

	## Bowtie2 indices.
	${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')}
    </command>

    <inputs>
        <param format="bam" name="accepted_hits" type="data" label="BAM file of aligned RNA-Seq reads" help=""/>
        <param format="tabular" name="fusions" type="data" label="Tabular file of potential fusions" help=""/>
        <param name="num_fusion_reads" type="integer" value="3" label="Num Fusion Reads" help="Fusions with at least this many supporting reads will be reported."/>
        <param name="num_fusion_pairs" type="integer" value="2" label="Num Fusion Pairs" help="Fusions with at least this many supporting pairs will be reported."/>
        <param name="num_fusion_both" type="integer" value="0" label="Num Fusion Reads + Pairs" help="The sum of supporting reads and pairs is at least this number for a fusion to be reported."/>
        <param name="fusion_read_mismatches" type="integer" value="2" label="Fusion Read Mismatches" help="Reads support fusions if they map across fusion with at most this many mismatches."/>
        <param name="fusion_multireads" type="integer" value="2" label="Reads that map to more than this many places will be ignored." help=""/>
        <param name="is_human" type="select" label="Is your data from humans?">
            <option value="Yes" selected="True">Yes</option>
            <option value="No">No</option>
        </param>
    </inputs>

    <stdio>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <outputs>
        <data format="txt" name="results_txt" label="${tool.name} on ${on_string}: text results" from_work_dir="tophatfusion_out/result.txt"/>
        <data format="html" name="results_html" label="${tool.name} on ${on_string}: html results" from_work_dir="tophatfusion_out/result.html"/>
    </outputs>
</tool>