comparison freebayes.xml @ 31:57def2d7c093 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"

30:ef2c525bd8cd

<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@">
    <description>bayesian genetic variant detector</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="4.1.3">gawk</requirement>

        ## REALIGNMENT
            ${options_type.O}

        ##INPUT FILTERS
            #if str( $options_type.input_filters.input_filters_selector ) == "set":
                ${options_type.input_filters.use_duplicate_reads}
                -m ${options_type.input_filters.m}
                -q ${options_type.input_filters.q}
                -R ${options_type.input_filters.R}
                -Y ${options_type.input_filters.Y}
                -e ${options_type.input_filters.e}
                -F ${options_type.input_filters.F}
                -C ${options_type.input_filters.C}
                -G ${options_type.input_filters.G}

                #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
                  -Q ${options_type.input_filters.mismatch_filters.Q}
                  #if str($options_type.input_filters.mismatch_filters.U)
                      -U ${options_type.input_filters.mismatch_filters.U}
                  #end if
                  -z ${options_type.input_filters.mismatch_filters.z}

                  --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
                #end if

                --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
            #end if

        ## POPULATION AND MAPPABILITY PRIORS
            #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
                ${options_type.population_mappability_priors.k}

                <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
                       label="Turn off left-alignment of indels" />

                <!-- input filters -->
                <conditional name="input_filters">
                    <param name="input_filters_selector" type="select" label="Input filters"
                           help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options">
                        <option value="do_not_set" selected="true">No input filters (default)</option>
                        <option value="set">Set input filters</option>
                    </param>
                    <when value="set">
                        <param name="use_duplicate_reads" argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
                               label="Include duplicate-marked alignments in the analysis" />
                        <param name="m" argument="--min-mapping-quality" type="integer" value="1"
                               label="Exclude alignments from analysis if they have a mapping quality less than" />
                        <param name="q" argument="--min-base-quality" type="integer" value="0"
                               label="Exclude alleles from analysis if their supporting base quality less than" />
                        <param name="R" argument="--min-supporting-allele-qsum" type="integer" value="0"
                               label="Consider any allele in which the sum of qualities of supporting observations is at least" />
                        <param name="Y" argument="--min-supporting-mapping-qsum" type="integer" value="0"
                               label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
                        <conditional name="mismatch_filters">
                            <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
                                   help="Sets -Q, -U, -z, and &#36; options">
                                <option value="do_not_set" selected="true">No mismatch filters (default)</option>
                                <option value="set">Set mismatch filters</option>
                            </param>
                            <when value="set">
                                <param name="Q" argument="--mismatch-base-quality-threshold" type="integer" value="10"
                                       label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
                                <param name="U" type="integer" argument="--read-mismatch-limit" value="1000" optional="true"
                                       label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
                                       help="default=~unbounded" />
                                <param name="z" argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
                                       label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
                                <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
                                       label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
                                       help="default=~unbounded" />
                            </when>
                            <when value="do_not_set" />
                        </conditional>
                        <param name="e" argument="--read-indel-limit" type="integer" value="1000"
                               label="Exclude reads with more than this number of separate gaps"
                               help="default=~unbounded" />
                        <param name="standard_filters" argument="--standard-filters" type="boolean" truevalue="-0" falsevalue="" checked="false"
                               label="Use stringent input base and mapping quality filters"
                               help="Equivalent to -m 30 -q 20 -R 0 -S 0" />
                        <param name="F" argument="--min-alternate-fraction" type="float" value="0.05"
                               label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
                        <param name="C" argument="--min-alternate-count" type="integer" value="2"
                               label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
                        <param name="min_alternate_qsum" argument="--min-alternate-qsum" type="integer" value="0"
                               label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
                        <param name="G" argument="--min-alternate-total" type="integer" value="1"
                               label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
                    </when>
                    <when value="do_not_set" />
                </conditional>

31:57def2d7c093

<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1">
    <description>bayesian genetic variant detector</description>
    <xrefs>
        <xref type="bio.tools">freebayes</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="4.1.3">gawk</requirement>

        ## REALIGNMENT
            ${options_type.O}

        ##INPUT FILTERS
            #if str( $options_type.input_filters.input_filters_selector ) == "set":
                $standard_filters
                ${options_type.input_filters.use_duplicate_reads}
                --min-mapping-quality ${options_type.input_filters.min_mapping_quality}
                --min-base-quality ${options_type.input_filters.min_base_quality}
                --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}
                --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}
                #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
                --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
                  #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
                    --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
                  #end if
                  --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
                  --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
                #end if
                --read-indel-limit ${options_type.input_filters.read_indel_limit}
                --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}
                --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
                --min-alternate-count ${options_type.input_filters.min_alternate_count}
                --min-alternate-total ${options_type.input_filters.min_alternate_total}
            #end if

        ## POPULATION AND MAPPABILITY PRIORS
            #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
                ${options_type.population_mappability_priors.k}

                <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
                       label="Turn off left-alignment of indels" />

                <!-- input filters -->
                <conditional name="input_filters">
                    <param name="input_filters_selector" type="select" label="Input filters">
                        <option value="do_not_set" selected="true">No input filters (default)</option>
                        <option value="set">Set input filters</option>
                    </param>
                    <when value="set">
                        <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"
                               label="Use stringent input base and mapping quality filters"
                               help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
                        <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
                               label="Include duplicate-marked alignments in the analysis" />
                        <param argument="--min-mapping-quality" type="integer" value="1"
                               label="Exclude alignments from analysis if they have a mapping quality less than" />
                        <param argument="--min-base-quality" type="integer" value="0"
                               label="Exclude alleles from analysis if their supporting base quality less than" />
                        <param argument="--min-supporting-allele-qsum" type="integer" value="0"
                               label="Consider any allele in which the sum of qualities of supporting observations is at least" />
                        <param argument="--min-supporting-mapping-qsum" type="integer" value="0"
                               label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
                        <conditional name="mismatch_filters">
                            <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
                                   help="Sets -Q, -U, -z, and &#36; options">
                                <option value="do_not_set" selected="true">No mismatch filters (default)</option>
                                <option value="set">Set mismatch filters</option>
                            </param>
                            <when value="set">
                                <param argument="--mismatch-base-quality-threshold" type="integer" value="10"
                                       label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
                                <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
                                       label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
                                       help="default=~unbounded" />
                                <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
                                       label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
                                <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
                                       label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
                                       help="default=~unbounded" />
                            </when>
                            <when value="do_not_set" />
                        </conditional>
                        <param argument="--read-indel-limit" type="integer" value="1000"
                               label="Exclude reads with more than this number of separate gaps"
                               help="default=~unbounded" />
                        <param argument="--min-alternate-fraction" type="float" value="0.05"
                               label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
                        <param argument="--min-alternate-qsum" type="integer" value="0"
                               label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
                        <param argument="--min-alternate-count" type="integer" value="2"
                               label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
                        <param argument="--min-alternate-total" type="integer" value="1"
                               label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
                    </when>
                    <when value="do_not_set" />
                </conditional>