annotate vcf2maf.xml @ 1:e8510e04a86a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vcf2maf commit f2287e6aab30c72ef1334688127711fc9624352e

<tool id="vcf2maf" name="Convert VCF to MAF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
	<description>with vcf2maf</description>
	<macros>
		<token name="@TOOL_VERSION@">1.6.21</token>
		<token name="@VERSION_SUFFIX@">1</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[
		## cBioPortal only supports human and mouse but requires their assembly name in NCBI format so we have to translate the dbkey for those
		#set $ncbi_names = {"hg19": "GRCh37", "hg38": "GRCh38", "mm10": "GRCm38", "mm39": "GRCm39"}

		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 #if $include_header then 'MainOutput.maf' else 'temp.maf'# --ref-fasta reference.fa
		#if $annotation_cache.source == "no_vep":
			--inhibit-vep
			#if $input1.metadata.dbkey in $ncbi_names:
				--ncbi-build '${ncbi_names[$input1.metadata.dbkey]}'
			#else:
				--ncbi-build '${input1.metadata.dbkey}'
			#end if
		#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
		#if not $include_header:
			&& tail -n+2 temp.maf > MainOutput.maf
		#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."/>
		<param name="include_header" type="boolean" checked="true" label="Include MAF version header in output file" help="The MAF version header is a comment that indicates the MAF version and is written into the first row of the ouput file. This is required by some downstream tools. The row containing column headers follows next."/>
		
		<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" />
			<assert_command>
				<has_text text="--ncbi-build 'GRCh37'"/>
			</assert_command>
			<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" />
			<assert_command>
				<has_text text="--ncbi-build 'GRCh37'"/>
			</assert_command>
			<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" />
			<param name="include_header" value="False" />
			<output name="output1" ftype="tabular" >
				<assert_contents>
					<has_n_lines n="2" />
					<not_has_text text="#version 2.4" />
				</assert_contents>
			</output>
		</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" />
			<assert_command>
				<has_text text="--ncbi-build 'BDGP6.32'"/>
			</assert_command>
			<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>