annotate varscan_mpileup2indel.xml @ 1:2c56a59a112f draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/galaxy-tool-shed-tools commit bd543e68c1af82bcd6a04f0ae3d1180e8887e122

<?xml version="1.0" encoding="UTF-8"?>
<tool id="varscan_mpileup2indel" name="VarScan2 Call INDELs from a mpileup file" version="2.4.2.a">
    <description>VarScan2 INDEL detection (on mpileup data)</description>
    
    <requirements>
        <requirement type="package" version="2.4.2">varscan</requirement>
    </requirements>
    
    <version_command>varscan 2&gt;&amp;1 | head -n 1</version_command>
    
    <command detect_errors="exit_code"><![CDATA[
        varscan mpileup2indel

        '${mpileup_input}'

            #if $extended_parameters.parameters == "extended"
                 --min-coverage     $extended_parameters.varscan_min_coverage
                 --min-reads2       $extended_parameters.varscan_min_reads2
                 --min-avg-qual     $extended_parameters.varscan_min_avg_qual
                 --min-var-freq     $extended_parameters.varscan_min_var_freq
                 --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
                 --p-value          $extended_parameters.varscan_p_value
                                    $extended_parameters.varscan_strand_filter 
                                    $extended_parameters.varscan_variants 
            #end if

            #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
                --output-vcf 1 
            #end if

            > '${snv_output}'
    ]]></command>
    
    <inputs>
        <param name="mpileup_input" format="pileup" type="data" label="Alignment file"
               help="Mapped reads in mpileup format."/>
        
        <conditional name="extended_parameters">
            <param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings.">
                <option value="default">Default settings</option>
                <option value="extended">Extended settings</option>
            </param>
            <when value="default">
            </when>
            <when value="extended">
                <param type="integer" name="varscan_min_coverage"     value="8"       label="Minimum read depth at a position to make a call [8]" />
                <param type="integer" name="varscan_min_reads2"	      value="2"       label="Minimum supporting reads at a position to call variants [2]" />
                <param type="integer" name="varscan_min_avg_qual"     value="15"      label="Minimum base quality at a position to count a read [15]" />
                <param type="float"   name="varscan_min_var_freq"     value="0.01"    label="minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" />
                <param type="float"   name="varscan_min_freq_for_hom" value="0.75"    label="Minimum frequency to call homozygote [0.75]" />
                <param type="float"   name="varscan_p_value"          value="0.99"    label="Default p-value threshold for calling variants [99e-02]" />
                <param type="boolean" name="varscan_strand_filter"    falsevalue=" --strand_filter 0" truevalue=" --strand_filter 1" checked="true"  label="VarScan: Ignore variants with >90% support on one strand [1]" />
                <param type="boolean" name="varscan_variants"         falsevalue=" --variants 0"      truevalue=" --variants 1"      checked="false" label="VarScan: Report only variant (SNP/indel) positions [0]" />
            </when>
        </conditional>
        
        <param name="varscan_output" type="select" label="Output format">
            <option value="vcf">VCF</option>
            <option value="tabular">tabular</option>
        </param>
    </inputs>
    
    <outputs>
        <data format="tabular" name="snv_output" label="${tool.name} on ${mpileup_input.hid}: ${mpileup_input.name}">
            <change_format>
                <when input="varscan_output" value="vcf" format="vcf" />
            </change_format>
        </data>
    </outputs>
    
    <tests>
        <test>
            <param name="mpileup_input" value="example.mpileup" ftype="pileup" />
            <param name="parameters" value="default" />
            <param name="varscan_output_vcf" value="1" />
            
            <output name="snv_output" file="example.vcf" />
        </test>
    </tests>
    
    <help>
**VarScan 2.4.2**

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems.
http://dx.doi.org/10.1101/gr.129684.111
http://www.ncbi.nlm.nih.gov/pubmed/19542151

**Input formats**

Alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing.

**Installation**

Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment.
</help>
    <citations>
        <citation type="doi">10.1101/gr.129684.111</citation>
    </citations>
</tool>