comparison cfsan_snp_pipeline_call_sites.xml @ 1:9ab66ea409ff draft

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0:02ab4f93ebd0

    <inputs>
        <param name="input" label="Read alignment to reference" type="data" format="bam"/>
        <param name="reference" label="FASTA Reference from your history" type="data" format="fasta"/>
    </inputs>
    <outputs>
        <data name="calls" label="${input.name.split(' ')[0]} unfiltered SNPs" format="vcf"/>
        <data name="pileup" label="${input.name.split(' ')[0]} pileup" format="pileup"/>
        <data name="metrics" label="Metrics from Picard" format="txt"/>
        <data label="S3 Cache log" name="cache_log" format="txt"/>
    </outputs>
    <tests>
        <test>
            <param name="reference" value="lambda_virus.fasta"/>
            <param name="input" value="reads.bam"/>
            <output name="calls" ftype="vcf">
                <assert_contents>
                    <has_size value="9976" delta="100"/>
        </assert_contents>
            </output>
            <output name="pileup" ftype="pileup">
                <assert_contents>
                    <has_size value="4259620" delta="100"/>
        </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>

1:9ab66ea409ff

    <inputs>
        <param name="input" label="Read alignment to reference" type="data" format="bam"/>
        <param name="reference" label="FASTA Reference from your history" type="data" format="fasta"/>
    </inputs>
    <outputs>
        <data name="calls" label="Call Sites (unfiltered SNPs)" format="vcf"/>
        <data name="pileup" label="Call Sites (pileup)" format="pileup"/>
        <data name="metrics" label="Call sites (Picard metrics)" format="txt"/>
    </outputs>
    <tests>
        <test>
            <param name="reference" value="lambda_virus.fasta"/>
            <param name="input" value="reads.bam"/>
            <output name="calls" ftype="vcf">
                <assert_contents>
                    <has_size value="9976" delta="100"/>
                </assert_contents>
            </output>
            <output name="pileup" ftype="pileup">
                <assert_contents>
                    <has_size value="4259620" delta="100"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
        <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>