view lofreq_call.xml @ 6:c208346da4be draft default tip

planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/lofreq commit 5a2f510980e0bdb7067e4a72d169a0431797ecc0-dirty

<tool id="lofreq_call" name="LoFreq Calling Variants" version="0.1.0">
    <requirements>
        <requirement type="package" version="2.1.3.1">lofreq</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        lofreq call
        -f "$input1"
        -o "$output1"
        #if $region and str($region) != '':
          -r "$region"
        #end if
        #if $RegionBedFile and str($RegionBedFile) != '':
          -l "$RegionBedFile"
        #end if
        --min-bq "$MinBq"
        --min-alt-bq "$MinAltBq"
        --def-alt-bq "$DefAltBq"
        --min-jq "$MinJq"
        --min-alt-jq "$MinAltJq"
        --def-alt-jq "$DefAltJq"
        #if $BaseAlignmentAndIndedAlignment and str($BaseAlignmentAndIndedAlignment) != '':
          #echo " "
          #echo ' '.join(str($BaseAlignmentAndIndedAlignment).split(','))
        #end if
        --min-mq "$MinMq"
        --max-mq "$MaxMq"
        --def-nm-q "$DefNmQ"
        --min-cov "$MinCov"
        --max-depth "$MaxDepth"
        --sig "$Sig"
        --bonf "$Bonf"
        --force-overwrite
        $merge_mapping_quality
        #if $sq_vcf and str($sq_vcf) != '':
          -S "$sq_vcf"
        #end if
        #if $indels and str($indels) != '':
          #echo " "
          #echo ' '.join(str($indels).split(','))
        #end if
        #if $misc and str($misc) != '':
          #echo " "
          #echo ' '.join(str($misc).split(','))
        #end if
        "$input2"
    ]]></command>
    <inputs>
        <param type="data" name="input2" format="bam" label="Input Bam File"/>
        <param type="data" name="input1" format="fa,fasta" label="Indexed reference fasta file (gzip supported)" help="Indexed reference fasta file (gzip supported)"/>
        <param name="region" type="text" label="Limit calls to this region (chrom:start-end)">
            <help>
               Limit calls to this region (chrom:start-end).
            </help>
            <validator type="regex" message="No whitespace allowed">^\S*$</validator>
        </param>
        <param format="bed" name="RegionBedFile" type="data" optional="true" label="List of positions (chr pos) or regions (BED) file"/>
	    <param name="MinBq" type="integer" label="Skip any base with baseQ smaller than" value="6" help="Skip any base with baseQ smaller than [INT]" />
        <param name="MinAltBq" type="integer" label="Skip alternate bases with baseQ smaller than" value="6" help=" Skip alternate bases with baseQ smaller than [INT]" />
        <param name="DefAltBq" type="integer" label="Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep)" value="0" help="Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [INT]" />
        <param name="MinJq" type="integer" label="Skip any base with joinedQ smaller than" value="0" help="Skip any base with joinedQ smaller than [INT]" />
        <param name="MinAltJq" type="integer" label="Skip alternate bases with joinedQ smaller than" value="0" help="Skip alternate bases with joinedQ smaller than [INT]" />
        <param name="DefAltJq" type="integer" label="Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep)" value="0" help="Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep)" />

        <param name="BaseAlignmentAndIndedAlignment" type="select" display="checkboxes" multiple="true" label="Base-alignment (BAQ) and indel-aligment (IDAQ) qualities Options">
            <option value="--no-baq">Disable use of base-alignment quality (BAQ)</option>
            <option value="--del-baq">Delete pre-existing BAQ values, i.e. compute even if already present in BAM</option>
            <option value="--no-ext-baq"> Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)</option>
        </param>
        <param name="MinMq" type="integer" label="Skip reads with mapping quality smaller than" value="0" help="Skip reads with mapping quality smaller than [INT]" />
        <param name="MaxMq" type="integer" label="Cap mapping quality at " value="0" help="Cap mapping quality at [INT]" />
        <param name="DefNmQ" type="integer" label="If >= 0, then replace non-match base qualities with this default value [-1] " value="0" help="   If >= 0, then replace non-match base qualities with this default value [-1]" />
        <param name="MinCov" type="integer" label="Test only positions having at least this coverage " value="1" help="(note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)" />
        <param name="MaxDepth" type="integer" label="Cap coverage at this depth" value="1000000" help="Cap coverage at this depth [1000000] [INT]" />

        <param name="merge_mapping_quality" type="boolean" truevalue="" falsevalue="--no-mq" checked="true" label="Don't merge mapping quality in LoFreq's model"/>
        <param format="vcf" name="sq_vcf" type="data" optional="true" label="Ignore variants in this vcf file for source quality computation."/>
        <param name="indels" type="select" display="checkboxes" multiple="true" label="Indels Options">
            <option value="--call-indels">Enable indel calls (note: preprocess your file to include indel alignment qualities!)</option>
            <option value="--only-indels">Only call indels; no SNVs</option>
        </param>

        <param name="Sig" type="float" label="P-Value cutoff / significance level [0.010000]" value="0.010000" help="P-Value cutoff / significance level [0.010000]" />
        <param name="Bonf" type="text" label="Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']" value="dynamic" help="Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']" />

        <param name="misc" type="select" display="checkboxes" multiple="true" label="Misc Options">
            <option value="--illumina-1.3">Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded</option>
            <option value="--verbose">Be verbose</option>
        </param>

    </inputs>
    <outputs>
        <data name="output1" format="vcf" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="ref.fa"/>
            <param name="input2" value="aln.bam"/>
            <output name="output1" file="vars.vcf"/>
        </test>
    </tests>
    <help><![CDATA[
        lofreq call: call variants from BAM file

Usage: lofreq call [options] in.bam

Options:
- Reference:
       -f | --ref FILE              Indexed reference fasta file (gzip supported) [null]
- Output:
       -o | --out FILE              Vcf output file [- = stdout]
- Regions:
       -r | --region STR            Limit calls to this region (chrom:start-end) [null]
       -l | --bed FILE              List of positions (chr pos) or regions (BED) [null]
- Base-call quality:
       -q | --min-bq INT            Skip any base with baseQ smaller than INT [6]
       -Q | --min-alt-bq INT        Skip alternate bases with baseQ smaller than INT [6]
       -R | --def-alt-bq INT        Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0]
       -j | --min-jq INT            Skip any base with joinedQ smaller than INT [0]
       -J | --min-alt-jq INT        Skip alternate bases with joinedQ smaller than INT [0]
       -K | --def-alt-jq INT        Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0]
- Base-alignment (BAQ) and indel-aligment (IDAQ) qualities:
       -B | --no-baq                Disable use of base-alignment quality (BAQ)
       -A | --no-idaq               Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)
       -D | --del-baq               Delete pre-existing BAQ values, i.e. compute even if already present in BAM
       -e | --no-ext-baq            Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)
- Mapping quality:
       -m | --min-mq INT            Skip reads with mapping quality smaller than INT [0]
       -M | --max-mq INT            Cap mapping quality at INT [255]
       -N | --no-mq                 Don't merge mapping quality in LoFreq's model
- Indels:
            --call-indels           Enable indel calls (note: preprocess your file to include indel alignment qualities!)
            --only-indels           Only call indels; no SNVs
- Source quality:
       -s | --src-qual              Enable computation of source quality
       -S | --ign-vcf FILE          Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas
       -T | --def-nm-q INT          If >= 0, then replace non-match base qualities with this default value [-1]
- P-values:
       -a | --sig                   P-Value cutoff / significance level [0.010000]
       -b | --bonf                  Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']
- Misc.:
       -C | --min-cov INT           Test only positions having at least this coverage [1]
                                    (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)
       -d | --max-depth INT         Cap coverage at this depth [1000000]
            --illumina-1.3          Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded
            --use-orphan            Count anomalous read pairs (i.e. where mate is not aligned properly)
            --plp-summary-only      No variant calling. Just output pileup summary per column
            --no-default-filter     Don't run default 'lofreq filter' automatically after calling variants
            --force-overwrite       Overwrite any existing output
            --verbose               Be verbose
            --debug                 Enable debugging

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githublofreq,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {lofreq},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/CSB5/lofreq},
}</citation>
    </citations>
</tool>