Mercurial > repos > iuc > beacon2_vcf2bff
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit eecd43b81a8c9f2175c50a71ae85ce9185a9d3a7
author | iuc |
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date | Tue, 16 Apr 2024 09:27:55 +0000 |
parents | 0a757835a745 |
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<tool id="beacon2_vcf2bff" name="Beacon2 VCF2BFF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>converting annotated VCF files to Beacon v2 format</description> <macros> <import>macros.xml</import> </macros> <expand macro="xrefs"/> <expand macro="requirements"/> <expand macro="creators"/> <command detect_errors="exit_code"><![CDATA[ ln -s '$input' ./sample.vcf.gz && vcf2bff.pl --input ./sample.vcf.gz --format '$format' --project-dir ./ --dataset-id '$dataset_id' --genome '$genome' && gunzip ./genomicVariationsVcf.json.gz ]]></command> <inputs> <param argument="--input" type="data" format="tabular.gz" label="Annotated vcf file" help="The output genomic variations VCF file of bcftools, snpeff, snpsift" /> <param argument="--format" type="select" label="Output format" help=""> <option value="bff" selected="True">BFF</option> <option value="hash">hash</option> <option value="json">json</option> </param> <param argument="--dataset-id" type="text" label="Dataset ID" value="" help="Give an ID for the created genomicVariations dataset" /> <param argument="--genome" type="text" label="Reference genome" value="" help="Select the reference genome used the annotate the data to create the genomicVariations dataset examples for reference genomes are hs37, hg37 and hg38" /> </inputs> <outputs> <data name="genomicVariationsVcf" format="json" label="${tool.name} on ${on_string}: genomicVariationsVcf file" from_work_dir="genomicVariationsVcf.json" /> </outputs> <tests> <test expect_num_outputs="1"> <param name="input" ftype="tabular.gz" value="test.vcf.gz" /> <param name="format" value="bff"/> <param name="dataset_id" value="beacon"/> <param name="genome" value="hg19"/> <output name="genomicVariationsVcf" file="genomicVariationsVcf.json" ftype="json" compare="sim_size"> <assert_contents><has_size value="730000" delta="90000" /></assert_contents> </output> </test> </tests> <help><![CDATA[ The tool Creates genomicVariations file from annotated genomic variations VCF file. The VCF file is annotated by using the workflow of those tools bcftools -> snpeff -> snpsift. The tool converts the annotated VCF file into genomicVariations entry type and serializes it as a JSON file also called Beacon Friendly Format (BFF). The generated file will be ready to be stored on the MongoDB instance as MongoDB works directly with JSON files. ]]></help> <expand macro="citations" /> </tool>