comparison vsnp_get_snps.xml @ 12:544b2ed99a9a draft

Uploaded

11:fa304dc06f12

mkdir -p $input_vcf_dir &&
mkdir -p $output_json_avg_mq_dir &&
mkdir -p $output_json_snps_dir &&
mkdir -p $output_snps_dir &&

#set dbkey = '?'
#for $i in $input_vcf_collection:
    #if str($dbkey) == '?':
        #set dbkey = $i.metadata.dbkey
    #else if str($dbkey) != $i.metadata.dbkey:
        >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique" && exit 1
    #end if
    #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
    ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' &&
#end for
#if str($dbkey) == '?':
    >&2 echo "The dbkey must be set for the zero coverage VCF files with SNPs found in closely related isolate groups" && exit 1
#end if
#if str($input_zc_vcf_type_cond.input_zc_vcf_type) == "single":
    #set zc_vcf_identifier = re.sub('[^\s\w\-]', '_', str($input_zc_vcf.element_identifier))
    ln -s '${input_zc_vcf}' '$input_vcf_dir/${zc_vcf_identifier}' &&
#else

            </when>
            <when value="collection">
                <param name="input_zc_vcf_collection" format="vcf" type="data_collection" collection_type="list" label="Collection of zero coverage VCF files"/>
            </when>
        </conditional>
        <param name="input_vcf_collection" format="vcf" type="data_collection" collection_type="list" label="Collection of zero coverage VCF files with SNPs found in closely related isolate groups"/>
        <param name="ac" type="integer" min="0" value="2" label="Allele count threshold" help="At least 1 position must have this value for a SNP to be added to a group"/>
        <param name="min_mq" type="integer" min="0" value="56" label="Map quality threshold" help="At least 1 position must have a higher MQ value for a SNP to be added to a group"/>
        <param name="min_quality_score" type="integer" min="0" value="150" label="Quality score threshold" help="At least 1 position must have a higher quality score for a SNP to be added to a group"/>
        <param name="quality_score_n_threshold" type="integer" min="0" value="150" label="Minimum quality score N value for alleles" help="Alleles are marked as N for quality scores between this value and the minimum quality score value above"/>
        <conditional name="input_excel_cond">

        -->
        <!-- A single vcf input, no excel file, all_isolates is False -->
        <test expect_num_outputs="4">
            <param name="input_zc_vcf_type" value="single"/>
            <param name="input_zc_vcf" value="input_zc_vcf.vcf" ftype="vcf" dbkey="89"/>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="SRR8073662_zc.vcf" value="SRR8073662_zc.vcf" dbkey="89"/>
                    <element name="SRR1792272_zc.vcf" value="SRR1792272_zc.vcf" dbkey="89"/>
                </collection>

                <collection type="list">
                    <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
                    <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
                </collection>
            </param>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
                    <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>

                <collection type="list">
                    <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
                    <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
                </collection>
            </param>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
                    <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>

                <collection type="list">
                    <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
                    <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
                </collection>
            </param>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
                    <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>

12:544b2ed99a9a

mkdir -p $input_vcf_dir &&
mkdir -p $output_json_avg_mq_dir &&
mkdir -p $output_json_snps_dir &&
mkdir -p $output_snps_dir &&

#if str($input_additional_zc_vcf_collection_cond.input_additional_zc_vcf_collection) =='yes':
    #set dbkey = '?'
    #for $i in $input_additional_zc_vcf_collection_cond.input_vcf_collection:
        #if str($dbkey) == '?':
            #set dbkey = $i.metadata.dbkey
        #else if str($dbkey) != $i.metadata.dbkey:
            >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique" && exit 1
        #end if
        #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
        ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' &&
    #end for
    #if str($dbkey) == '?':
        >&2 echo "The dbkey must be set for the zero coverage VCF files with SNPs found in closely related isolate groups" && exit 1
    #end if
#end if
#if str($input_zc_vcf_type_cond.input_zc_vcf_type) == "single":
    #set zc_vcf_identifier = re.sub('[^\s\w\-]', '_', str($input_zc_vcf.element_identifier))
    ln -s '${input_zc_vcf}' '$input_vcf_dir/${zc_vcf_identifier}' &&
#else

            </when>
            <when value="collection">
                <param name="input_zc_vcf_collection" format="vcf" type="data_collection" collection_type="list" label="Collection of zero coverage VCF files"/>
            </when>
        </conditional>
        <conditional name="input_additional_zc_vcf_collection_cond">
            <param name="input_additional_zc_vcf_collection" type="select" label="Include an additional collection of curated zero-coverage VCF files?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="input_vcf_collection" format="vcf" type="data_collection" collection_type="list" label="Collection of zero coverage VCF files with SNPs found in closely related isolate groups"/>
            </when>
        </conditional>
        <param name="ac" type="integer" min="0" value="2" label="Allele count threshold" help="At least 1 position must have this value for a SNP to be added to a group"/>
        <param name="min_mq" type="integer" min="0" value="56" label="Map quality threshold" help="At least 1 position must have a higher MQ value for a SNP to be added to a group"/>
        <param name="min_quality_score" type="integer" min="0" value="150" label="Quality score threshold" help="At least 1 position must have a higher quality score for a SNP to be added to a group"/>
        <param name="quality_score_n_threshold" type="integer" min="0" value="150" label="Minimum quality score N value for alleles" help="Alleles are marked as N for quality scores between this value and the minimum quality score value above"/>
        <conditional name="input_excel_cond">

        -->
        <!-- A single vcf input, no excel file, all_isolates is False -->
        <test expect_num_outputs="4">
            <param name="input_zc_vcf_type" value="single"/>
            <param name="input_zc_vcf" value="input_zc_vcf.vcf" ftype="vcf" dbkey="89"/>
            <param name="input_additional_zc_vcf_collection" value="yes"/>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="SRR8073662_zc.vcf" value="SRR8073662_zc.vcf" dbkey="89"/>
                    <element name="SRR1792272_zc.vcf" value="SRR1792272_zc.vcf" dbkey="89"/>
                </collection>

                <collection type="list">
                    <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
                    <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
                </collection>
            </param>
            <param name="input_additional_zc_vcf_collection" value="yes"/>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
                    <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>

                <collection type="list">
                    <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
                    <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
                </collection>
            </param>
            <param name="input_additional_zc_vcf_collection" value="yes"/>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
                    <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>

                <collection type="list">
                    <element name="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" value="BCG_Pasteur_Unknown_FR_SRR8886989.vcf" dbkey="89"/>
                    <element name="BCG_Tokyo_Unknown_JP_DRR029468.vcf" value="BCG_Tokyo_Unknown_JP_DRR029468.vcf" dbkey="89"/>
                </collection>
            </param>
            <param name="input_additional_zc_vcf_collection" value="yes"/>
            <param name="input_vcf_collection">
                <collection type="list">
                    <element name="01_1787_FL_Zoo_Jaguar.vcf" value="01_1787_FL_Zoo_Jaguar.vcf" dbkey="89"/>
                    <element name="02_5877_MEX_TX_Fed.vcf" value="02_5877_MEX_TX_Fed.vcf" dbkey="89"/>
                    <element name="02_0585_COA_TX_Fed.vcf" value="02_0585_COA_TX_Fed.vcf" dbkey="89"/>