view vt_normalize.xml @ 0:26babe3a66f1 draft default tip

planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0

<tool id="vt_@BINARY@" name="VT @BINARY@" version="@VERSION@.0">
    <description>normalizes variants in a VCF file</description>
    <macros>
        <import>vt_macros.xml</import>
        <token name="@BINARY@">normalize</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[
        vt @BINARY@
            #if str($output_format) == 'bcf':
                -o normalised.bcf
            #else:
                -o normalised.vcf
            #end if
            ##-q  do not print options and summary []
            -w $window

            #if str( $intervals_file ) != 'None':
                -I  "${intervals_file}"
            #end if
            $n
            ##-i  intervals []

            #if $reference_source.reference_source_selector != "history":
                -r "${reference_source.reference_genome.fields.path}"
            #else:
                -r "${reference_source.reference_genome}"
            #end if

            "${ infile }"

        &&
        ## For some reason, the file move will randomly produce empty files.
        ## Wait two seconds to let the system close file handlers and clean up.
        sleep 2
        &&

        #if str($output_format) == 'bcf':
            mv normalised.bcf "${ outfile }";
        #else:
            mv normalised.vcf "${ outfile }";
        #end if

]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="vcf" label="VCF file to be normalised" />

        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
                <option value="cached" selected="True">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="reference_genome" type="select" label="Using reference genome">
                    <options from_data_table="fasta_indexes">
                        <filter type="data_meta" ref="infile" key="dbkey" column="1" />
                        <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference_genome" type="data" format="fasta" label="Using reference file" />
            </when>
        </conditional>
        <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" />
        <param name="window" type="integer" value="10000" label="Window size for local sorting of variants"
            help="(-w)">
            <validator type="in_range" min="0"/>
        </param>
        <param argument="-n" type="boolean" truevalue="-n" falsevalue=""
            label="Do not fail when REF is inconsistent with reference sequence for non SNPs"
            help=""/>
        <param name="output_format" type="select" label="Choose the output format" help="">
            <option value="bcf">BCF</option>
            <option value="vcf" selected="true">VCF</option>
        </param>
    </inputs>
    <outputs>
        <data name="outfile" format="vcf" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="output_format" value="bcf" format="bcf" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="infile01.vcf" />
            <param name="reference_source_selector" value="history" />
            <param name="reference_genome" value="20.fa.bz2" />
            <param name="n" value="True" />
            <output name="outfile" file="normalize_result01.vcf" ftype="vcf" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

Normalize variants in a VCF file. Normalized variants may have their positions changed; in such cases,
the normalized variants are reordered and output in an ordered fashion. The local reordering takes place over a window of 10000 base pairs.

@CITATION@
]]>
    </help>
    <expand macro="citations"/>
</tool>