annotate distance.xml @ 5:b69e898b8109 draft

planemo upload for repository https://github.com/phac-nml/quasitools commit e30c0687f755a46c5b3bd265a1478a1abf5dc9f1

<tool id="distance" name="Quasispecies Distance" version="0.4.2">
    <description>Calculate the evolutionary distance between viral quasispecies.</description>
    <requirements>
          <requirement type="package" version="0.4.2">quasitools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

        #for $bam_file in $bam_files
        ln -s $bam_file '${bam_file.name}' &&
        ln -s $bam_file.metadata.bam_index '${bam_file.name}.bai' &&
        #end for

        quasitools distance $ref_file

        #for $bam_file in $bam_files
        '${bam_file.name}'
        #end for

        -o matrix.csv

        $normalize

        #if $low_coverage.coverage_selector == 'keep':
            -k
        #else if $low_coverage.coverage_selector == 'remove':
            -r
        #else if $low_coverage.coverage_selector == 'truncate':
            -t
        #end if

        #if $select_range.manual_input == 'select_range':
            -s $select_range.start
            -e $select_range.end
        #end if

        $output_similarity

    ]]></command>
    <inputs>
        <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
        <param name="bam_files" type="data" format="bam" optional="false" multiple="true" label="BAM files" min="2" help="At least two BAM files are required to perform quasispecies distance comparison."/>
        <param name="normalize" type="boolean" truevalue="-n" falsevalue="-dn" checked="True" label="Normalize pileups" help="Normalize read count data so that the read counts per 4-tuple (A, C, T, G) sum to one."/>
        <param name="output_similarity" type="boolean" truevalue="-os" falsevalue="-od" checked="False" label="Output cosine similarity instead of angular cosine distance." help="Cosine similarity is not a distance metric." />
        <conditional name="low_coverage">
            <param name="coverage_selector" type="select" label="Choose how to treat zero coverage positions.">
                <option value="remove" selected = "true">Remove all zero coverage positions.</option>
                <option value="keep">Keep all zero coverage positions.</option>
                <option value="truncate">Truncate zero coverage positions at start and end of pileup.</option>
            </param>
            <when value="remove">
            </when>
            <when value="keep">
            </when>
            <when value="truncate">
            </when>
        </conditional>
        <conditional name="select_range">
            <param name="manual_input" type="select" label="Select pileup range." help="Currently only supports selection of custom start and end position for one single reference.">
                <option value="keep_range" selected = "true">Use original pileup for distance calculation.</option>
                <option value="select_range">Manually select pileup's start and end position for distance calculation.</option>
            </param>
            <when value="select_range">
                <param name="start" type="integer" optional="false" min="1" value="1" label="Select one-indexed start base position." help="Positions before start position will be ignored in the distance calculation." />
                <param name="end" type="integer" optional="false" min="1" value="1" label="Select one-indexed end base position." help="Positions after end position will be ignored in the distance calculation." />
            </when>
            <when value="keep_range">
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="csv" name="matrix" from_work_dir="matrix.csv" />
    </outputs>
    <tests>
        <test>
            <param name="ref_file" value="hxb2_pol.fas" />
            <param name="bam_files" value="quasi1.bam,quasi2.bam" />
            <param name="normalize" value="-n" />
            <param name="coverage_selector" value="truncate" />
            <param name="manual_input" value="keep_range" />
            <param name="output_similarity" value="-od" />
            <output name="matrix" ftype="csv" >
                <assert_contents>
                    <has_text_matching expression="Quasispecies"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Quasispecies Distance
=====================

Determines the evolutionary distance between viral quasispecies.
Uses the angular cosine distance function by default.

------
Inputs
------

1. FASTA Consensus file
2. Two or more BAM files (otherwise tool will throw an error)

----------
Parameters
----------
1. Normalize pileup (True or False)
2. Select custom start and end position. Currently only supports selection of custom start and end position for one single reference.
3. Choose how to treat zero coverage regions (keep, remove all, or truncate)

-------
Outputs
-------

CSV containing distance matrix.

    ]]></help>
    <citations>
        <citation type="bibtex">
            @misc{GitHubquasitoolsdistance,
            title = {quasitools distance},
            publisher = {phac-nml},
            journal = {GitHub repository},
            url = {https://github.com/phac-nml/quasitools},
            }
        </citation>
    </citations>
</tool>