comparison tophat_fusion_post.xml @ 2:3279e193b966 draft default tip

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

1:ae4ed992d98a

<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=""/>

    <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>

2:3279e193b966

<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" version="2.2.28">blast+</requirement>
        <requirement type="package" version="0.12.7">bowtie</requirement>
        <requirement type="package" version="2.0.9">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 \${GALAXY_SLOTS:-4}
        --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

	    ## Bowtie indices.
	    ${__get_data_table_entry__('bowtie_indexes', 'value', $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=""/>

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

    <outputs>
        <data format="tabular" 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>