annotate varscan_mpileup2snp_from_bam.xml @ 1:9a39c4105901 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_mpileup2snp_from_bam" name="VarScan2 Call SNPs from BAM" version="2.4.2.a">
    <description>VarScan2 SNP/SNV detection; directly reading *.bam file(s) &amp; using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.</description>
    
    <requirements>
        <requirement type="package" version="2.4.2">varscan</requirement>
        <requirement type="package" version="0.6.5">sambamba</requirement>
    </requirements>
    
    <version_command>varscan 2&gt;&amp;1 | head -n 1</version_command>
    
    <command detect_errors="exit_code"><![CDATA[
        #for $alignment in $alignments
            ln -f -s '${alignment.metadata.bam_index}' '${alignment}.bai' &&
        #end for
        
        sambamba mpileup
            -t \${GALAXY_SLOTS:-4}
            
            #for $alignment in $alignments
                 '${alignment}'
            #end for
            
            --samtools
                -f
                #if $reference_genome_source.source_select == "indexed_filtered"
                    '$reference_genome_source.reference_genome'
                #else if $reference_genome_source.source_select == "indexed_all"
                    '$reference_genome_source.reference_genome'
                #else if $reference_genome_source.source_select == "history"
                    '$reference_genome_source.reference_genome'
                #else
                    <!--
                        This is a workaround to obtain the "genome.fa" file that
                        corresponds to the dbkey of the alignments.
                        Because this file is "calculated" during run-time, it can
                        be used in a workflow.
                    -->
                    "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
                #end if

                #if $extended_parameters_regions.sambamba_regions == "region"
                     -r '${extended_parameters_regions.sambamba_r}'
                #elif $extended_parameters_regions.sambamba_regions == "regions_file_pos" or $extended_parameters_regions.sambamba_regions == "regions_file_bed"
                     -l '${extended_parameters_regions.sambamba_l}'
                #end if

                #if $extended_parameters.parameters == "extended"
                    $extended_parameters.sambamba_6
                    $extended_parameters.sambamba_A
                    $extended_parameters.sambamba_B
                     -C $extended_parameters.sambamba_C
                     -d $extended_parameters.sambamba_d
                    $extended_parameters.sambamba_E
                     -M $extended_parameters.sambamba_M
                    $extended_parameters.sambamba_R
                     -q $extended_parameters.sambamba_q
                     -Q $extended_parameters.sambamba_Q

                     -e $extended_parameters.sambamba_e
                     -F $extended_parameters.sambamba_F
                     -h $extended_parameters.sambamba_h
                    $extended_parameters.sambamba_I
                     -L $extended_parameters.sambamba_L
                     -m $extended_parameters.sambamba_m
                     -o $extended_parameters.sambamba_o
                    $extended_parameters.sambamba_p
                     -P $extended_parameters.sambamba_P
                #end if
            | varscan mpileup2snp
             
                #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 format="bam,sam" multiple="true" name="alignments" type="data" label="Alignment file(s)" help="Mapped reads in BAM or SAM format."/>
        
        <!-- Find out how to access the reference genome from the BAM file(s) -->
        <conditional name="reference_genome_source">
            <param name="source_select" type="select" label="Fasta Source">
                <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
                <option value="history">Use reference from the history</option>
                <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option>
                <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>
            </param>
            <when value="history">
                <param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (FASTA)" help="Reference genome (genome.fa) that corresponds to the *.bam file." />
            </when>
            <when value="indexed_filtered">
                <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" >
                    <options from_data_table="all_fasta">
                        <column name="name"  index="2"/>
                        <column name="dbkey" index="1"/>
                        <column name="value" index="3"/><!-- Value is the path of the fasta file -->
                        <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" />
                        <validator type="no_options" message="No indexes are available for the selected input dataset" />
                    </options>
                </param>
            </when>
            <when value="indexed_all">
                <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" >
                    <options from_data_table="all_fasta">
                        <column name="name"  index="2"/>
                        <column name="dbkey" index="1"/>
                        <column name="value" index="3"/><!-- Value is the path of the fasta file -->
                        <validator type="no_options" message="No indexes are available for the selected input dataset" />
                    </options>
                </param>
            </when>
            <when value="attribute" />
        </conditional>
        
        <conditional name="extended_parameters_regions">
            <param name="sambamba_regions" type="select" label="Region specific parameters" help="Let sambamba target specific genomic locations.">
                <option value="entire_genome">Entire genome</option>
                <option value="region">Specific region</option>
                <option value="regions_file_pos">Specific positions (file); list of positions</option>
                <option value="regions_file_bed">Specific regions (file); list of regions in BED</option>
            </param>
            <when value="entire_genome" />
            <when value="region">
                <param type="text" name="sambamba_r" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:pos or chr:start-end" />
            </when>
            <when value="regions_file_pos">
                <param type="data" name="sambamba_l" format="tabular" label="Samtools: list of positions (chr pos)" />
            </when>
            <when value="regions_file_bed">
                <param type="data" name="sambamba_l" format="bed"     label="Samtools: specific regions (BED)" />
            </when>
        </conditional>
        
        <conditional name="extended_parameters">
            <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and sambamba settings.">
                <option value="default">Default settings</option>
                <option value="extended">Extended settings</option>
            </param>
            <when value="default" />
            <when value="extended">
                <param type="boolean" name="sambamba_6" falsevalue="" truevalue=" -6" label="Samtools: assume the quality is in the Illumina-1.3+ encoding" />
                <param type="boolean" name="sambamba_A" falsevalue="" truevalue=" -A" label="Samtools: count anomalous read pairs" />
                <param type="boolean" name="sambamba_B" falsevalue="" truevalue=" -B" label="Samtools: disable BAQ computation" />
                <param type="integer" name="sambamba_C" value="0"                     label="Samtools: parameter for adjusting mapQ; 0 to disable [0]" />
                <param type="integer" name="sambamba_d" value="250"                   label="Samtools: max per-BAM depth to avoid excessive memory usage [250]" />
                <param type="boolean" name="sambamba_E" falsevalue="" truevalue=" -E" label="Samtools: recalculate extended BAQ on the fly thus ignoring existing BQs" />
                <param type="integer" name="sambamba_M" value="60"                    label="cap mapping quality at INT [60]" />
                <param type="boolean" name="sambamba_R" falsevalue="" truevalue=" -R" label="Samtools: ignore RG tags" />
                <param type="integer" name="sambamba_q" value="0"                     label="Samtools: skip alignments with mapQ smaller than INT [0]" />
                <param type="integer" name="sambamba_Q" value="13"                    label="Samtools: skip bases with baseQ/BAQ smaller than INT [13]" />
                
                <param type="integer" name="sambamba_e" value="20"                    label="Samtools: Phred-scaled gap extension seq error probability [20]" />
                <param type="float"   name="sambamba_F" value="0.002"                 label="Samtools: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" />
                <param type="integer" name="sambamba_h" value="100"                   label="Samtools: coefficient for homopolymer errors [100]" />
                <param type="boolean" name="sambamba_I" falsevalue="" truevalue=" -I" label="Samtools: do not perform indel calling" />
                <param type="integer" name="sambamba_L" value="250"                   label="Samtools: max per-sample depth for INDEL calling [250]" />
                <param type="integer" name="sambamba_m" value="1"                     label="Samtools: minimum gapped reads for indel candidates [1]" help="Alias: -m" />
                <param type="integer" name="sambamba_o" value="40"                    label="Samtools: Phred-scaled gap open sequencing error probability [40]" />
                <param type="boolean" name="sambamba_p" falsevalue="" truevalue=" -p" label="Samtools: apply -m and -F per-sample to increase sensitivity" />
                <param type="text"    name="sambamba_P" value="all"                   label="Samtools: comma separated list of platforms for indels [all]" />
                
                <param type="integer" name="varscan_min_coverage"     value="8"       label="VarScan: Minimum read depth at a position to make a call [8]" />
                <param type="integer" name="varscan_min_reads2"	      value="2"       label="VarScan: PMinimum supporting reads at a position to call variants [2]" />
                <param type="integer" name="varscan_min_avg_qual"     value="15"      label="VarScan: Minimum base quality at a position to count a read [15]" />
                <param type="float"   name="varscan_min_var_freq"     value="0.01"    label="VarScan: 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="VarScan: Minimum frequency to call homozygote [0.75]" />
                <param type="float"   name="varscan_p_value"          value="0.99"    label="VarScan: 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 ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}">
            <change_format>
                <when input="varscan_output" value="vcf" format="vcf" />
            </change_format>
        </data>
    </outputs>
    
    <tests>
        <test><!-- Use classical sambamba -->
            <param name="alignments" value="example.bam" ftype="bam" />
            
            <param name="source_select" value="history" />
            <param name="reference_genome" value="example.fa" />
            
            <param name="sambamba_regions" value="entire_genome" />
            
            <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.
http://dx.doi.org/10.1101/gr.129684.111
http://www.ncbi.nlm.nih.gov/pubmed/19542151

*VarScan* requires mpileup input files, generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing can be by-passed using this tool.
Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan.

.. _VarScan: http://varscan.sourceforge.net/

**Input formats**

VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/).
The alignment files must have a reference genome (dbkey) in Galaxy.

Contact
-------

The tool wrapper has been written by Youri Hoogstrate from the Erasmus
Medical Center (Rotterdam, Netherlands) 
</help>
    <citations>
        <citation type="doi">10.1101/gr.129684.111</citation>
    </citations>
</tool>