comparison arriba.xml @ 3:2d32e6c86c48 draft

"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit b4882afed9ec678b576f126907094c77c03eae96"

2:7420753b0671

    #if '$tags'
        -t '$tags'
    #end if
    -o fusions.tsv
    -O fusions.discarded.tsv 
    ]]></command>
    <inputs>
        <conditional name="input_params">
            <param name="input_source" type="select" label="Use output from earlier STAR run or let Arriba running STAR">
                <option value="use_star">Use output from earlier STAR</option>

                </conditional>
            </when>
        </conditional>
        <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/>
        <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/>
        <param name="blacklist" argument="-b" type="data" format="tabular" label="File containing blacklisted ranges."/>
        <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing blacklisted ranges."/>
        <param name="known_fusions" argument="-k" type="data" format="tabular"  optional="true" label="File containing known fusions">
            <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
        </param>
        <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."/>
    </inputs>
    <outputs>
        <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>
        <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"/>
    </outputs>
    <help><![CDATA[
** Arriba **

3:2d32e6c86c48

    #if '$tags'
        -t '$tags'
    #end if
    -o fusions.tsv
    -O fusions.discarded.tsv 
#if str($input_params.input_source) == "use_fastq"
    && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam
    && samtools index Aligned.sortedByCoord.out.bam
#elif str($visualization.do_viz) == "yes"
    && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam
    && samtools index Aligned.sortedByCoord.out.bam
#end if
#if str($visualization.do_viz) == "yes"
draw_fusions.R \
    --fusions=fusions.tsv 
    --alignments=Aligned.sortedByCoord.out.bam 
    --output=fusions.pdf 
    --annotation='$gtf'
    #if $visualization.cytobands
    --cytobands='$visualization.cytobands'
    #end if
    #if '$protein_domains'
    --proteinDomains=database/protein_domains_hg19_hs37d5_GRCh37_v2.1.0.gff3
    #end if
#end if

    ]]></command>
    <inputs>
        <conditional name="input_params">
            <param name="input_source" type="select" label="Use output from earlier STAR run or let Arriba running STAR">
                <option value="use_star">Use output from earlier STAR</option>

                </conditional>
            </when>
        </conditional>
        <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/>
        <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/>
        <param name="blacklist" argument="-b" type="data" format="tabular" optional="true" label="File containing blacklisted ranges."/>
        <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing blacklisted ranges."/>
        <param name="known_fusions" argument="-k" type="data" format="tabular"  optional="true" label="File containing known fusions">
            <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help>
        </param>
        <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."/>
        <conditional name="visualization">
            <param name="do_viz" type="select" label="Generate visualization">
                <option value="yes">Yes</option>
                <option value="no">no</option>
            </param>
            <when value="yes">
                <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
            </when>
            <when value="no"/>
        </conditional>
        
    </inputs>
    <outputs>
        <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/>
        <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"/>
        <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
            <filter>input_params['input_source'] == "use_fastq"</filter>
        </data> 
        <data name="fusions_png" format="png" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
            <filter>visualization['do_viz'] == "yes"</filter>
        </data> 
    </outputs>
    <help><![CDATA[
** Arriba **