comparison arriba.xml @ 3:2eca65b822be draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 7943aa76786271a466aa1b0e2c8fac3f32176863

2:eb3200075443

        -Z $options.min_itd_supporting_reads
    #end if
    $options.duplicate_marking
    $options.fill_discarded_columns
    $options.fill_the_gaps
#if str($visualization.do_viz) == "yes"
    && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam
    && samtools index Aligned.sortedByCoord.out.bam
#end if
#if $output_fusions_vcf
    && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf

        </data> 
        <collection name="fusion_bams" type="list" label="${tool.name} on ${on_string}: Fusion Alignments">
            <discover_datasets pattern="(?P&lt;name&gt;fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/>
            <filter>output_fusion_bams == True</filter>
        </collection>
        <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
            <filter>input_params['input_source'] == "use_fastq"</filter>
        </data> 
        <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
            <filter>visualization['do_viz'] == "yes"</filter>
        </data> 
    </outputs>
    <tests>
        <!-- Test 1 - From exisitng BAM -->
        <test> 
            <param name="input" ftype="sam" value="Aligned.out.sam"/>
            <conditional name="genome">
                <param name="genome_source" value="history"/>
                <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
            </conditional>

                    <has_text_matching expression="BCR\tABL1"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test 2 - From exisitng BAM with protein_domains and visualization -->
        <test> 
            <param name="input" ftype="sam" value="Aligned.out.sam"/>
            <conditional name="genome">
                <param name="genome_source" value="history"/>
                <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
            </conditional>

3:2eca65b822be

        -Z $options.min_itd_supporting_reads
    #end if
    $options.duplicate_marking
    $options.fill_discarded_columns
    $options.fill_the_gaps
#if $output_fusion_bams or str($visualization.do_viz) == "yes"
    && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input' > Aligned.sortedByCoord.out.bam
    && samtools index Aligned.sortedByCoord.out.bam
#end if
#if $output_fusions_vcf
    && convert_fusions_to_vcf.sh '$genome_assembly' fusions.tsv fusions.vcf

        </data> 
        <collection name="fusion_bams" type="list" label="${tool.name} on ${on_string}: Fusion Alignments">
            <discover_datasets pattern="(?P&lt;name&gt;fusion_\d+\.bam)$" format="bam" directory="fusion_bams" visible="false"/>
            <filter>output_fusion_bams == True</filter>
        </collection>
        <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf">
            <filter>visualization['do_viz'] == "yes"</filter>
        </data> 
    </outputs>
    <tests>
        <!-- Test 1 - From exisitng BAM -->
        <test expect_num_outputs="3"> 
            <param name="input" ftype="sam" value="Aligned.out.sam"/>
            <conditional name="genome">
                <param name="genome_source" value="history"/>
                <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
            </conditional>

                    <has_text_matching expression="BCR\tABL1"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test 2 - From exisitng BAM with protein_domains and visualization -->
        <test expect_num_outputs="4"> 
            <param name="input" ftype="sam" value="Aligned.out.sam"/>
            <conditional name="genome">
                <param name="genome_source" value="history"/>
                <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
            </conditional>