Mercurial > repos > iuc > geneiobio
view geneiobio-iframe.xml @ 0:c0af7b196a89 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
author | iuc |
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date | Thu, 29 Jun 2023 08:33:46 +0000 |
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children | fc53fcdbe548 |
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<tool id="gene_iobio_display_generation_iframe" name="gene.iobio visualisation" version="4.7.1"> <description>analyses VCFs for single and trio analysis to find causative variants using gene.iobio's public server</description> <command>cat '$index' | tr -d '\n' > '$outfile'</command> <configfiles> <configfile name="index"><![CDATA[ <html> <body> <iframe src="https://gene.iobio.io/?genes=${genes} &species=Human &build=${refgen_version} &affectedSibs= &unaffectedSibs= &rel0=proband &sex0=${proband_sex} &vcf0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/display &tbi0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index #if $proband_bam.ext == 'bam': &bam0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display &bai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index #elif $proband_bam.ext == 'cram': &cram0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display &cai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index #end if &sample0=${proband_name} &affectedStatus0=${proband_affected} #if str( $input_type.input_type_selector ) == "trio"# &rel1=father &sex1=male &vcf1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/display &tbi1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index #if $input_type.father.bam.ext == 'bam': &bam1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display &bai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index #elif $input_type.father.bam.ext == 'cram': &cram1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display &cai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index #end if &sample1=${input_type.father.name} &affectedStatus1=${input_type.father.affected} &rel2=mother &sex2=female &vcf2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/display &tbi2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index #if $input_type.mother.bam.ext == 'bam': &bam2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display &bai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index #elif $input_type.mother.bam.ext == 'cram': &cram2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display &cai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index #end if &sample2=${input_type.mother.name} &affectedStatus2=${input_type.mother.affected} #end if " style="width: 100%; height: 900px;"></iframe> </body></html> ]]></configfile> </configfiles> <inputs> <param name="proband_vcf" type="data" format="vcf,vcf_bgzip" label="Proband VCF file"/> <param name="proband_bam" type="data" format="bam,cram" label="Proband BAM file" optional="true"/> <param name="proband_sex" type="select" display="radio" label="Proband sex"> <option value="male" selected="true">Male</option> <option value="female">Female</option> </param> <param name="proband_affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="true" label="Is the proband affected?"/> <param name="proband_name" type="text" value="C" label="Proband sample name" help="The sample names are listed in the columns of the VCF."/> <conditional name="input_type"> <param name="input_type_selector" type="select" display="radio" label="Single/Trio analysis"> <option value="single" selected="true">Single</option> <option value="trio">Trio</option> </param> <when value="trio"> <section name="father" title="Father input"> <param name="vcf" type="data" format="vcf,vcf_bgzip" label="Father VCF file"/> <param name="bam" type="data" format="bam,cram" label="Father BAM file" optional="true"/> <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the father affected?"/> <param name="name" type="text" value="F" label="Father sample name" help="The sample names are listed in the columns of the VCF."/> </section> <section name="mother" title="Mother input"> <param name="vcf" type="data" format="vcf,vcf_bgzip" label="Mother VCF file"/> <param name="bam" type="data" format="bam,cram" label="Mother BAM file" optional="true"/> <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the mother affected?"/> <param name="name" type="text" value="M" label="Mother sample name" help="The sample names are listed in the columns of the VCF."/> </section> </when> <when value="single"> </when> </conditional> <param name="genes" type="text" value="PDHA1,ARHGAP8,RAI1,PLXNA1,SCN8A,SMARCA2" size="100x5" label="Genes of interest" help="Provide the genes as a comma seperated line. This line can be empty and genes can be selected interactively using gene.iobio."/> <param name="refgen_version" type="select" label="Select reference genome version"> <option value="GRCh38" selected="true">GRCh38</option> <option value="GRCh37">GRCh37</option> </param> </inputs> <outputs> <data name="outfile" format="html" /> </outputs> <tests> <!-- Test 1 - Single --> <test expect_num_outputs="1"> <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/> <param name="proband_bam" ftype="bam" value="proband.bam" /> <param name="proband_sex" ftype="text" value="female" /> <param name="proband_name" ftype="text" value="Case5C" /> <param name="genes" ftype="text" value="BRCA1" /> <param name="refgen_version" ftype="text" value="GRCh37" /> <output name="outfile"> <assert_contents> <has_size value= "659" delta="100" /> </assert_contents> </output> </test> <!-- Test 2 - Trio --> <test expect_num_outputs="1"> <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/> <param name="proband_bam" ftype="bam" value="proband.bam" /> <param name="proband_sex" ftype="text" value="female" /> <param name="proband_name" ftype="text" value="Case5C" /> <param name="genes" ftype="text" value="BRCA1" /> <param name="refgen_version" ftype="text" value="GRCh37" /> <conditional name="input_type"> <param name="input_type_selector" value="trio"/> <section name="mother"> <param name="vcf" ftype="vcf" value="family.vcf.gz"/> <param name="bam" ftype="bam" value="mother.bam" /> <param name="affected" ftype="text" value="affected" /> <param name="name" ftype="text" value="Case5M" /> </section> <section name="father"> <param name="vcf" ftype="vcf" value="family.vcf.gz"/> <param name="bam" ftype="bam" value="father.bam" /> <param name="affected" ftype="text" value="unaffected" /> <param name="name" ftype="text" value="Case5F" /> </section> </conditional> <output name="outfile"> <assert_contents> <has_size value= "1555" delta="500" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ Gene.iobio provides a report of impactful variants. Gene.iobio also helps prioritize variants based on multiple integrated gene:disease association algorithms and knowledge bases. .. class:: Warning mark This transfers data to a remote server, in US jurisdiction. In order to do this make sure to make the history accessible, i.e. anyone with a link can reach the data. Required inputs: 1. Proband VCF file Optional inputs (trio analysis): 1. Proband BAM file 2. Father & Mother BAM file 3. Father & Mother VCF file The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_. .. _iobio project: https://iobio.io .. _Marth lab: https://marthlab.org/ .. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/ ]]></help> <citations> <citation type="doi">10.1038/s41598-021-99752-5</citation> </citations> </tool>