annotate galaxy/tools/config_builder/config_builder.xml @ 7:4bfb3a8dd955 draft

Bug fixes

<tool id="config_builder" name="PathOGiST - Config Builder" version="1.0.0">
    <description>: Creates and populates the config file to run PathOGiST</description>
    <requirements>
        <requirement type="package" version="0.3">pathogist</requirement>
    </requirements>

    <command><![CDATA[
        $__tool_directory__/config_builder

        #if $snippy.snippy_checkbox
            --snippy
            --reference $snippy.reference
            #if $snippy.snippy_adv.snippy_adv_checkbox
                --mapqual $snippy.snippy_adv.mapqual
                --basequal $snippy.snippy_adv.basequal
                --mincov $snippy.snippy_adv.mincov
                --minfrac $snippy.snippy_adv.minfrac
            #end if
            $snippy.snp_fine
            --snp_thresh $snippy.snp_threshold
        #end if

        #if $mentalist.mentalist_checkbox
            --mentalist
            #if $mentalist.db_loc.db_selector == "local_file"
                --local_file
                --local_db $mentalist.db_loc.mlst_database
            #end if
            #if $mentalist.db_loc.db_selector == "build_db"
                --build_db
                --kmer $mentalist.db_loc.k
                --fasta_files $mentalist.db_loc.fasta_files
                --profile $mentalist.db_loc.profile
            #end if
            #if $mentalist.db_loc.db_selector == "download_pubmlst"
                --download_pubmlst
                --kmer $mentalist.db_loc.k
                --scheme $mentalist.db_loc.scheme
            #end if
            #if $mentalist.db_loc.db_selector == "download_cgmlst"
                --download_cgmlst
                --kmer $mentalist.db_loc.k
                --scheme $mentalist.db_loc.scheme
            #end if
            #if $mentalist.db_loc.db_selector == "download_enterobase"
                --download_enterobase $mentalist.db_loc.k
                --entero_scheme $mentalist.db_loc.scheme
                --entero_type $mentalist.db_loc.type
            #end if
            #if $mentalist.mentalist_adv.mentalist_adv_checkbox
                --mutation_threshold $mentalist.mentalist_adv.mutation_thresh
                --kt $mentalist.mentalist_adv.kt
            #end if
            $mentalist.mlst_fine
            --mlst_thresh $mentalist.mlst_threshold
        #end if

        #if $prince.prince_checkbox
            --prince
            $prince.cnv_fine
            --cnv_thresh $prince.cnv_threshold
        #end if

        #if $kwip.kwip_checkbox
            --kwip
            #if $kwip.kwip_adv.kwip_adv_checkbox
                --N $kwip.kwip_adv.N
                --x $kwip.kwip_adv.x
                --ksize $kwip.kwip_adv.ksize
                --unique_kmers $kwip.kwip_adv.unique_kmers
            #end if
            $kwip.kwip_fine
            --kwip_thresh $kwip.kwip_threshold
        #end if

        #if $spotyping.spotyping_checkbox
            --spotyping
            $spotyping.spoligo_fine
            --spoligo_thresh $spotyping.spoligo_threshold
        #end if

        #if $adv_clustering.adv_clustering_checkbox
            $adv_clustering.all_constraints
            --method $adv_clustering.method
            $adv_clustering.presolve
            $adv_clustering.visualize
        #end if

        $forward
        $reverse
        config.yaml
    ]]></command>


    <inputs>
        <param name="forward" type="data" format="txt,tabular" label="List of forward reads"/>
        <param name="reverse" type="data" format="txt,tabular" label="List of reverse reads"/>

        <conditional name="snippy">
            <param name="snippy_checkbox" type="boolean" label="Run Snippy"/>
            <when value="true">
                <param name="reference" type="data" format="fasta,fa,fasta.gz,fa.gz" label="Reference Genome"/>
                <conditional name="snippy_adv">
                    <param name="snippy_adv_checkbox" type="boolean" label="Advanced Snippy Parameters"/>
                    <when value="true">
                        <param name="mapqual" type="integer" value="60" min="0" label="Minimum read mapping
                        quality to consider"/>
                        <param name="basequal" type="integer" value="20" min="0" label="Minimum base quality
                        to consider"/>
                        <param name="mincov" type="integer" value="10" min="0" label="Minimum coverage of
                        variant site"/>
                        <param name="minfrac" type="float" value="0.9" min="0" label="Minimum proportion of
                        variant evidence"/>
                    </when>
                </conditional>
                <param name="snp_fine" type="boolean" checked="true" falsevalue="" truevalue="--fine_snp"
                       label="Consider SNP as a fine datatype"/>
                <param name="snp_threshold" type="integer" value="2500" min="0"
                       label="Correlation clustering threshold for MLST"/>
            </when>
        </conditional>

        <conditional name="mentalist">
            <param name="mentalist_checkbox" type="boolean" label="Run MentaLiST"/>
            <when value="true">
                <conditional name="db_loc">
                    <param name="db_selector" type="select" label="Option for obtaining MLST database">
                        <option value="local_file">Local File</option>
                        <option value="build_db">Build DB</option>
                        <option value="download_pubmlst">Download PubMLST Scheme</option>
                        <option value="download_cgmlst">Download cgMLST Scheme</option>
                        <option value="download_enterobase">Download Enterobase Scheme</option>
                    </param>
                    <when value="local_file">
                        <param name="mlst_database" format="db" type="data" label="MLST database file"/>
                    </when>
                    <when value="build_db">
                        <param name="k" type="integer" value="31" min="1" label="kmer size"/>
                        <param name="fasta_files" type="data" format="txt,tabular" label="List of FASTA files"/>
                        <param name="profile" type="data" format="txt" label="Profile file for known
                        genotypes"/>
                    </when>
                    <when value="download_pubmlst">
                        <param name="k" type="integer" value="31" min="1" label="kmer size"/>
                        <param name="scheme" type="text" label="Species name or scheme ID"/>
                    </when>
                    <when value="download_cgmlst">
                        <param name="k" type="integer" value="31" min="1" label="kmer size"/>
                        <param name="scheme" type="text" label="Species name or scheme ID"/>
                    </when>
                    <when value="download_enterobase">
                        <param name="k" type="integer" value="31" min="1" label="kmer size"/>
                        <param name="scheme" type="text" label="(S)almonella, (Y)ersinia, or
                        (E)scherichia/Shigella"/>
                        <param name="type" type="text" label="'cg' or 'wg' for cgMLST or wgMLST, respectively"/>
                    </when>
                </conditional>

                <conditional name="mentalist_adv">
                    <param name="mentalist_adv_checkbox" type="boolean" label="Advanced MentaLiST Parameters"/>
                    <when value="true">
                        <param name="mutation_thresh" type="integer" min="1" value="6" label="Maximum number of
                        mutations when looking for novel alleles"/>
                        <param name="kt" type="integer" value="10" min="1" label="Minimum number of times a
                        kmer is seen to be considered present in the sample"/>
                    </when>
                </conditional>
                <param name="mlst_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_mlst"
                       label="Consider MLST as a fine datatype"/>
                <param name="mlst_threshold" type="integer" value="300" min="0"
                       label="Correlation clustering threshold for MLST"/>
            </when>
        </conditional>

        <conditional name="prince">
            <param name="prince_checkbox" type="boolean" label="Run PRINCE"/>
            <when value="true">
                <param name="cnv_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_cnv"
                       label="Consider CNV as a fine datatype"/>
                <param name="cnv_threshold" type="integer" value="100" min="0"
                       label="Correlation clustering threshold for CNV"/>
            </when>
        </conditional>

        <conditional name="kwip">
            <param name="kwip_checkbox" type="boolean" label="Run kWIP"/>
            <when value="true">
                <conditional name="kwip_adv">
                    <param name="kwip_adv_checkbox" type="boolean" label="Advanced kWIP Parameters"/>
                    <when value="true">
                        <param name="N" type="integer" value="1" min="1" label="Number of tables"/>
                        <param name="x" type="float" value="1e9" min="1" label="Maximum table size"/>
                        <param name="ksize" type="integer" value="31" min="1" label="kmer size"/>
                        <param name="unique_kmers" type="integer" value="0" min="0" label="Approximate number
                        of unique kmers in the input set"/>
                    </when>
                </conditional>
                <param name="kwip_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_kwip"
                       label="Consider kWIP as a fine datatype"/>
                <param name="kwip_threshold" type="float" value="0.4" min="0"
                       label="Correlation clustering threshold for kWIP"/>
            </when>
        </conditional>

        <conditional name="spotyping">
            <param name="spotyping_checkbox" type="boolean" label="Run SpoTyping"/>
            <when value="true">
                <param name="spoligo_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_spoligo"
                       label="Consider spoligotype as a fine datatype"/>
                <param name="spoligo_threshold" type="integer" value="8" min="0"
                       label="Correlation clustering threshold for Spoligotyping"/>
            </when>
        </conditional>

        <conditional name="adv_clustering">
            <param name="adv_clustering_checkbox" type="boolean"
                   label="Advanced settings for correlation and consensus clustering"/>
            <when value="true">
                <param name="all_constraints" type="boolean" checked="true" falsevalue="--less_constraints"
                       truevalue="" label="Use all constraints when performing clustering"/>
                <param name="method" type="text" value="C4" size="3"
                       label="`C4` or `ILP` method for clustering algorithm"/>
                <param name="presolve" type="boolean" checked="true" falsevalue="--no_presolve" truevalue=""
                       label="Perform presolving for clustering"/>
                <param name="visualize" type="boolean" checked="false" falsevalue="" truevalue="--visualize"
                       label="Visualize clusters"/>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="output" label="PathOGiST Config File" format="yaml" from_work_dir="config.yaml"/>
    </outputs>

    <help>

    </help>

    <citations>

    </citations>
</tool>