view qc.xml @ 4:e34ab51fa707 draft

"planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/qc commit c11a408ecf1ea81fcca4bac8d503ee2731077722"

<tool id="qc_cog_uk" name="Quality Control (COG-UK QC)" version="0.1.0" python_template_version="3.5">
    <requirements>
        <requirement type="package" version="1.11">samtools</requirement>
        <requirement type="package" version="1.78">biopython</requirement>
        <requirement type="package" version="1.2.3">pandas</requirement>
        <requirement type="package" version="3.3.4">matplotlib</requirement>
    </requirements>
    <command detect_errors="exit_code" interpreter="python"><![CDATA[
        qc.py '$qc_type_conditional.qc_type' 
            --outfile '$output1' 
            --sample '$input_sample'
            --ref '$input_ref' 
            --bam '$input_bam' 
            --fasta '$input_cons_fasta' && 
        mv '$input_sample'.depth.png '$output2'
    ]]></command>
    <inputs>
        <conditional name="input_type_conditional">
            <param name="input_type" type="select" label="Input Type">
                <option value="single" selected="true">Single Dataset</option>
                <option value="paired_collection">Paired Collection</option>
            </param>
            <when value="single">
                 <param name="input_sample" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
            </when>
            <when value="paired_collection">
                 <param name="input_sample" format="fastqsanger" type="data_collection" collection_type="paired" label="Select dataset pair" help="Specify paired dataset collection containing paired reads"/>
            </when>
        </conditional>
        <conditional name="qc_type_conditional">
            <param name="qc_type" type="select" label="Input Type">
                <option value="--illumina" selected="true">Illumina</option>
                <option value="--nanopore">Nanopore</option>
            </param>
        </conditional>
        <param type="data" name="input_ref" format="fasta" label="Reference File"/>
        <param type="data" name="input_bam" format="bam" label="Aligned (and trimmed) BAM "/>
        <param type="data" name="input_cons_fasta" format="fasta" label="Computed FASTA consensus"/>
    </inputs>
    <outputs>
        <data name="output1" format="csv" label="${tool.name} on ${on_string}: tubular output"/>
        <data name="output2" format="png" label="${tool.name} on ${on_string}: depth and density"/>
    </outputs>
    <tests>
        <test>
            <param name="input_sample" value="test_sample.fastqsanger.gz"/>
            <param name="input_ref" value="ref.fasta"/>
            <param name="input_bam" value="sample.bam"/>
            <param name="input_cons_fasta" value="sample_consensus.fasta"/>
            <output name="output1" file="test_sample.qc.csv"/>
            <output name="output2" file="test_sample.depth.png"/>
        </test>
    </tests>
    <help><![CDATA[
usage: qc.py [-h] (--nanopore | --illumina) --outfile OUTFILE --sample SAMPLE
        --ref REF --bam BAM --fasta FASTA
optional arguments:
-h, --help         show this help message and exit
--nanopore
--illumina
--outfile OUTFILE
--sample SAMPLE
--ref REF
--bam BAM
--fasta FASTA

        ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubncov2019-artic-nf,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {ncov2019-artic-nf},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/connor-lab/ncov2019-artic-nf},
}</citation>
    </citations>
</tool>