annotate ngsap-vc/gatk/gatk_macros.xml @ 3:0d10255b5434 draft default tip

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<macros>

    <xml name="requirements">
        <requirements>
            <requirement type="package">gatk</requirement>
            <requirement type="set_environment">GATK_PATH</requirement>
            <requirement type="set_environment">GATK_SITE_OPTIONS</requirement>
            <requirement type="package" version="3.1.2.1">package_r_for_gatk_3_4_0</requirement>
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command><![CDATA[ @GATK_EXEC@ --help|grep '^The Genome' ]]></version_command>
    </xml>

    <token name="@VERSION@">3.4-0</token>
    <token name="@OUTPUT_NAME_PREFIX@">${tool.name} - ${analysis_type.analysis_type_selector}</token>
    <token name="@GATK_EXEC@">
<![CDATA[
        #if $cond_threads.cond_threads_enabled:
            #if int($cond_threads.nct) > 1:
                THREAD_STRING="-nct $cond_threads.nct" &&
            #end if
            #if int($cond_threads.nt) > 1:
                THREAD_STRING=$THREAD_STRING" -nt $cond_threads.nt" &&
            #end if
            #if int($cond_threads.mem) > 0:
                GATK_MEM=$cond_threads.mem &&
            #end if
        #end if
        java -Xmx\${GATK_MEM:-\${SLURM_MEM_PER_NODE:-4096}}M -jar "\$GATK_PATH/GenomeAnalysisTK.jar" \${THREAD_STRING:-}
]]>
    </token>

    <xml name="macro_vcf_input" tokens="tag">
        <param name="input" type="data" format="vcf" multiple="true" label="Variant files (VCF format)" help="-V, &#8209;&#8209;variant">
            <validator type="unspecified_build" />
            <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> 
        </param>
    </xml>
    <token name="@token_vcf_input_pre@" tokens="tag">
<![CDATA[
        ############################
        ## create links to gVCF input files with correct extensions
        ############################
        #for $i, $variant in enumerate($analysis_type.input):
            ln -s -f ${variant} variant_${i}.vcf &&
        #end for
]]>
    </token>
    <token name="@token_vcf_input@">
<![CDATA[
        #for $i, $variant in enumerate($analysis_type.input):
            --variant variant_${i}.vcf
        #end for
        @token_reference_input@
]]>
    </token>


    <xml name="macro_gvcf_input" tokens="tag">
        <param name="input" type="data" format="vcf" multiple="true" label="Variant files (gVCF format)" help="-V, &#8209;&#8209;variant">
            <validator type="unspecified_build" />
            <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> 
        </param>
    </xml>
    <token name="@token_gvcf_input_pre@" tokens="tag">
<![CDATA[
        ############################
        ## create links to gVCF input files with correct extensions
        ############################
        #for $i, $variant in enumerate($analysis_type.input):
            ln -s -f ${variant} variant_${i}.g.vcf &&
        #end for
]]>
    </token>
    <token name="@token_gvcf_input@">
<![CDATA[
        #for $i, $variant in enumerate($analysis_type.input):
            --variant variant_${i}.g.vcf
        #end for
        @token_reference_input@
]]>
    </token>

    <xml name="macro_bam_input">
        <conditional name="cond_bam_input">
            <param name="all_in_one" type="boolean" value="false" label="Input all BAM files in a single command" />
            <when value="true">
                <param name="input" type="data" format="bam" multiple="true" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file">
                    <validator type="unspecified_build"/>
                    <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/>
                </param>
            </when>
            <when value="false">
                <param name="input" type="data" format="bam" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file">
                    <validator type="unspecified_build"/>
                    <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/>
                </param>
            </when>
        </conditional>
    </xml>
    <token name="@token_bam_input_pre@">
<![CDATA[
        ############################
        ## create links to bam input files with correct extensions
        ############################
        #if $analysis_type.cond_bam_input.all_in_one
            #for $i, $bam in enumerate($analysis_type.cond_bam_input.input):
                ln -s -f ${bam} input_${i}.bam &&
                ln -s -f ${bam.metadata.bam_index} input_${i}.bam.bai &&
            #end for
        #else
            ln -s -f ${analysis_type.cond_bam_input.input} input.bam &&
            ln -s -f ${analysis_type.cond_bam_input.input.metadata.bam_index} input.bam.bai &&
        #end if
]]>
    </token>
    <token name="@token_bam_input@">
<![CDATA[
        #if $analysis_type.cond_bam_input.all_in_one
            #for $i, $bam in enumerate($analysis_type.cond_bam_input.input):
                --input_file input_${i}.bam
            #end for
        #else
            --input_file            input.bam
        #end if
        @token_reference_input@
]]>
    </token>

    <token name="@token_reference_input@">
<![CDATA[
]]>
    </token>
    <xml name="macro_input" tokens="tag">
        <yield />
    </xml>

    <xml name="macro_optional_parameters">
        <conditional name="optional_parameters">
            <param name="optional_parameters_enabled" type="boolean" label="Configure Optional Parameters" />
            <when value="true">
                <yield />
            </when>
            <when value="false" />
        </conditional>
    </xml>

    <xml name="macro_advanced_parameters">
        <conditional name="advanced_parameters">
            <param name="advanced_parameters_enabled" type="boolean" label="Configure Advanced Parameters" />
            <when value="true">
                <yield />
            </when>
            <when value="false" />
        </conditional>
    </xml>

    <xml name="macro_tests">
        <tests>
            
        </tests>
    </xml>

</macros>