<tool id="vcf2maf" name="Convert VCF to MAF" version="@TOOL_VERSION@">
	<description>with vcf2maf</description>
	<macros>
		<token name="@TOOL_VERSION@">1.6.21</token>
		<token name="@DB_VERSION@">106</token>
	</macros>
	<requirements>
		<requirement type="package" version="@TOOL_VERSION@">vcf2maf</requirement>
		<requirement type="package" version="@DB_VERSION@.1">ensembl-vep</requirement>
	</requirements>
	<command detect_errors="exit_code"><![CDATA[
		ln -s '${input1}' MainInput.vcf &&
		#if $ref_seq.ref_source == "cached":
			ln -s '${ref_seq.ref.fields.path}' reference.fa &&
		#elif $ref_seq.ref_source == "history":
			ln -s '${ref_seq.ref}' reference.fa &&
		#end if
		vcf2maf.pl --input-vcf MainInput.vcf --output-maf MainOutput.maf --ref-fasta reference.fa
		#if $annotation_cache.source == "no_vep":
			--inhibit-vep
		#else:
			--vep-path \$(dirname \$(which vep))
			--vep-data '${annotation_cache.cache_file.fields.path}'
			--species '${annotation_cache.cache_file.fields.species}'
			--ncbi-build '${annotation_cache.cache_file.fields.value.split($annotation_cache.cache_file.fields.version + "_")[-1]}'
			#if $annotation_cache.cache_file.fields.version != "@DB_VERSION@": --cache-version $annotation_cache.cache_file.fields.version
		#end if

		#if $tumor_id:
			--tumor-id '${tumor_id}'
		#end if
		#if $normal_id:
			--normal-id '${normal_id}'
		#end if
		#if $vcf_tumor_id:
			--vcf-tumor-id '${vcf_tumor_id}'
		#end if
		#if $vcf_normal_id:
			--vcf-normal-id '${vcf_normal_id}'
		#end if

		#if $adv_opt.any_allele:
			--any-allele
		#end if
		#if $adv_opt.min_hom_vaf:
			--min-hom-vaf $adv_opt.min_hom_vaf
		#end if
		#if $adv_opt.maf_center:
			--maf-center '${adv_opt.maf_center}'
		#end if
		#if $adv_opt.retain_info:
			--retain-info '${adv_opt.retain_info}'
		#end if
		#if $adv_opt.retain_fmt:
			--retain-fmt '${adv_opt.retain_fmt}'
		#end if
		#if $adv_opt.retain_ann:
			--retain-ann '${adv_opt.retain_ann}'
		#end if
	]]></command>
	<inputs>
		<param type="data" name="input1" label="VCF input file" format="vcf">
			<validator type="unspecified_build" />
		</param>
		<conditional name="ref_seq">
			<param name="ref_source" type="select" label="Select FASTA file as reference sequence">
				<option value="cached">Locally cached</option>
				<option value="history">History</option>
			</param>
			<when value="cached">
				<param name="ref" type="select" label="Select reference sequence">
					<options from_data_table="fasta_indexes">
						<validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
					</options>
				</param>
			</when>
			<when value="history">
				<param name="ref" type="data" format="fasta" label="Select reference sequence" />
			</when>
		</conditional>
		<conditional name="annotation_cache">
			<param name="source" type="select" label="Select the source of annotation data if you want to use VEP" help="vcf2maf can utilize Ensembl's VEP to select a single effect per variant. VEP can only be used if SIFT is available for the selected genome assembly. Ensembl strongly recommends to only use annotation cache files with a version number matching the VEP version. You can disable the corresponding filtering of available cache files at your own risk.">
				<option value="no_vep" selected="true">Do not use VEP</option>
				<option value="restricted">Use VEP with a cache file with matching version number</option>
				<option value="unrestricted">Use VEP with any cache file</option>
			</param>
			<when value="no_vep"/>
			<when value="restricted">
				<param name="cache_file" type="select" label="Select annotation cache file" help="If the annotation data of interest is not listed, have a look at all available cache files regardless of their version number or contact your Galaxy admin.">
					<options from_data_table="vep_versioned_annotation_cache">
						<filter type="static_value" value="@DB_VERSION@" column="2" />
						<filter type="sort_by" column="4"/>
					</options>
					<validator type="no_options" message="No annotation caches are available"/>
				</param>
			</when>
			<when value="unrestricted">
				<param name="cache_file" type="select" label="Select annotation cache file" help="If the annotation data of interest is not listed, contact your Galaxy admin.">
					<options from_data_table="vep_versioned_annotation_cache">
						<filter type="sort_by" column="4"/>
					</options>
					<validator type="no_options" message="No annotation caches are available"/>
				</param>
			</when>
		</conditional>
		
		<param argument="--tumor-id" type="text" optional="true" label="Enter tumor sample ID (optional)" help="Used to fill the Tumor_Sample_Barcode column of the output MAF with the tumor sample ID."/>
		<param argument="--normal-id" type="text" optional="true" label="Enter normal sample ID (optional)" help="Used to fill the Matched_Norm_Sample_Barcode column of the output MAF with the normal sample ID."/>
		<param argument="--vcf-tumor-id" type="text" optional="true" label="Enter name of tumor genotype column (optional)" help="VCFs from variant callers like VarScan use hardcoded sample IDs TUMOR/NORMAL to name genotype columns. Use this parameter to have vcf2maf correctly locate these columns to parse genotypes, while still printing proper sample IDs in the output MAF."/>
		<param argument="--vcf-normal-id" type="text" optional="true" label="Enter name of normal genotype column (optional)" help="VCFs from variant callers like VarScan use hardcoded sample IDs TUMOR/NORMAL to name genotype columns. Use this parameter to have vcf2maf correctly locate these columns to parse genotypes, while still printing proper sample IDs in the output MAF."/>
		
		<section name="adv_opt" title="Advanced options">
			<param argument="--any-allele" type="boolean" optional="true" checked="false" label="Allow also mismatched variant alleles when reporting co-located variants"/>
			<param argument="--min-hom-vaf" type="float" optional="true" min="0" max="1" label="Enter minimum allele fraction to call a variant homozygous if GT is undefined in VCF" help="Default value is 0.7"/>
			<param argument="--maf-center" type="text" optional="true" label="Enter variant calling center to report in MAF"/>
			<param argument="--retain-info" type="text" optional="true" label="Enter comma-delimited names of INFO fields to retain as extra columns in MAF"/>
			<param argument="--retain-fmt" type="text" optional="true" label="Enter comma-delimited names of FORMAT fields to retain as extra columns in MAF"/>
			<param argument="--retain-ann" type="text" optional="true" label="Enter comma-delimited names of VEP annotations (within the VEP CSQ/ANN) to retain as extra columns in MAF"/>
		</section>
	</inputs>
	<outputs>
		<data name="output1" format="tabular" from_work_dir="MainOutput.maf" />
	</outputs>
	<tests>
		<test expect_num_outputs="1">
			<param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
			<param name="ref_source" value="history" />
			<param name="ref" dbkey="hg19" value="test1.fa" ftype="fasta" />
			<param name="annotation_cache.source" value="no_vep" />
			<output name="output1" file="output_test1.tabular" ftype="tabular" />
		</test>
		<test expect_num_outputs="1">
			<param name="input1" dbkey="hg19" value="input_test1.vcf" ftype="vcf" />
			<param name="ref_source" value="cached" />
			<param name="ref" value="hg19test" />
			<param name="annotation_cache.source" value="no_vep" />
			<output name="output1" file="output_test1.tabular" ftype="tabular" />
		</test>
		<test expect_num_outputs="1">
			<param name="input1" dbkey="dm6" value="input_test2.vcf" ftype="vcf" />
			<param name="ref_source" value="history" />
			<param name="ref" dbkey="dm6" value="test2.fa" ftype="fasta" />
			<param name="source" value="restricted" />
			<param name="cache_file" value="drosophila_melanogaster_vep_106_BDGP6.32" />
			<output name="output1" file="output_test2.tabular" ftype="tabular" />
		</test>
	</tests>
	<help><![CDATA[
		The tool vcf2maf can parse a wide range of VCF-like formats and convert these into the `Mutation Annotation Format (MAF) <https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/>`__. A central part of the conversion process is the selection of a single effect per variant. While this is often a subjective decision, vcf2maf offers a standardized way to achieve this by optionally utilizing Ensembl's `Variant Effect Predictor (VEP) <https://www.ensembl.org/info/docs/tools/vep/index.html>`__.	]]></help>
	<citations>
		<citation type="doi">10.5281/zenodo.593251</citation>
	</citations>
</tool>