Mercurial > repos > iuc > geneiobio
comparison geneiobio-iframe.xml @ 0:c0af7b196a89 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
| author | iuc |
|---|---|
| date | Thu, 29 Jun 2023 08:33:46 +0000 |
| parents | |
| children | fc53fcdbe548 |
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| -1:000000000000 | 0:c0af7b196a89 |
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| 1 <tool id="gene_iobio_display_generation_iframe" name="gene.iobio visualisation" version="4.7.1"> | |
| 2 <description>analyses VCFs for single and trio analysis to find causative variants using gene.iobio's public server</description> | |
| 3 <command>cat '$index' | tr -d '\n' > '$outfile'</command> | |
| 4 <configfiles> | |
| 5 <configfile name="index"><![CDATA[ | |
| 6 <html> | |
| 7 <body> | |
| 8 <iframe src="https://gene.iobio.io/?genes=${genes} | |
| 9 &species=Human | |
| 10 &build=${refgen_version} | |
| 11 &affectedSibs= | |
| 12 &unaffectedSibs= | |
| 13 &rel0=proband | |
| 14 &sex0=${proband_sex} | |
| 15 &vcf0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/display | |
| 16 &tbi0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index | |
| 17 #if $proband_bam.ext == 'bam': | |
| 18 &bam0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display | |
| 19 &bai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index | |
| 20 #elif $proband_bam.ext == 'cram': | |
| 21 &cram0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display | |
| 22 &cai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index | |
| 23 #end if | |
| 24 &sample0=${proband_name} | |
| 25 &affectedStatus0=${proband_affected} | |
| 26 #if str( $input_type.input_type_selector ) == "trio"# | |
| 27 &rel1=father | |
| 28 &sex1=male | |
| 29 &vcf1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/display | |
| 30 &tbi1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index | |
| 31 #if $input_type.father.bam.ext == 'bam': | |
| 32 &bam1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display | |
| 33 &bai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index | |
| 34 #elif $input_type.father.bam.ext == 'cram': | |
| 35 &cram1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display | |
| 36 &cai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index | |
| 37 #end if | |
| 38 &sample1=${input_type.father.name} | |
| 39 &affectedStatus1=${input_type.father.affected} | |
| 40 &rel2=mother | |
| 41 &sex2=female | |
| 42 &vcf2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/display | |
| 43 &tbi2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index | |
| 44 #if $input_type.mother.bam.ext == 'bam': | |
| 45 &bam2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display | |
| 46 &bai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index | |
| 47 #elif $input_type.mother.bam.ext == 'cram': | |
| 48 &cram2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display | |
| 49 &cai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index | |
| 50 #end if | |
| 51 &sample2=${input_type.mother.name} | |
| 52 &affectedStatus2=${input_type.mother.affected} | |
| 53 #end if | |
| 54 " style="width: 100%; height: 900px;"></iframe> | |
| 55 </body></html> | |
| 56 ]]></configfile> | |
| 57 </configfiles> | |
| 58 <inputs> | |
| 59 <param name="proband_vcf" type="data" format="vcf,vcf_bgzip" label="Proband VCF file"/> | |
| 60 <param name="proband_bam" type="data" format="bam,cram" label="Proband BAM file" optional="true"/> | |
| 61 <param name="proband_sex" type="select" display="radio" label="Proband sex"> | |
| 62 <option value="male" selected="true">Male</option> | |
| 63 <option value="female">Female</option> | |
| 64 </param> | |
| 65 <param name="proband_affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="true" label="Is the proband affected?"/> | |
| 66 <param name="proband_name" type="text" value="C" label="Proband sample name" help="The sample names are listed in the columns of the VCF."/> | |
| 67 <conditional name="input_type"> | |
| 68 <param name="input_type_selector" type="select" display="radio" label="Single/Trio analysis"> | |
| 69 <option value="single" selected="true">Single</option> | |
| 70 <option value="trio">Trio</option> | |
| 71 </param> | |
| 72 <when value="trio"> | |
| 73 <section name="father" title="Father input"> | |
| 74 <param name="vcf" type="data" format="vcf,vcf_bgzip" label="Father VCF file"/> | |
| 75 <param name="bam" type="data" format="bam,cram" label="Father BAM file" optional="true"/> | |
| 76 <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the father affected?"/> | |
| 77 <param name="name" type="text" value="F" label="Father sample name" help="The sample names are listed in the columns of the VCF."/> | |
| 78 </section> | |
| 79 <section name="mother" title="Mother input"> | |
| 80 <param name="vcf" type="data" format="vcf,vcf_bgzip" label="Mother VCF file"/> | |
| 81 <param name="bam" type="data" format="bam,cram" label="Mother BAM file" optional="true"/> | |
| 82 <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the mother affected?"/> | |
| 83 <param name="name" type="text" value="M" label="Mother sample name" help="The sample names are listed in the columns of the VCF."/> | |
| 84 </section> | |
| 85 </when> | |
| 86 <when value="single"> | |
| 87 </when> | |
| 88 </conditional> | |
| 89 <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."/> | |
| 90 <param name="refgen_version" type="select" label="Select reference genome version"> | |
| 91 <option value="GRCh38" selected="true">GRCh38</option> | |
| 92 <option value="GRCh37">GRCh37</option> | |
| 93 </param> | |
| 94 </inputs> | |
| 95 <outputs> | |
| 96 <data name="outfile" format="html" /> | |
| 97 </outputs> | |
| 98 <tests> | |
| 99 <!-- Test 1 - Single --> | |
| 100 <test expect_num_outputs="1"> | |
| 101 <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/> | |
| 102 <param name="proband_bam" ftype="bam" value="proband.bam" /> | |
| 103 <param name="proband_sex" ftype="text" value="female" /> | |
| 104 <param name="proband_name" ftype="text" value="Case5C" /> | |
| 105 <param name="genes" ftype="text" value="BRCA1" /> | |
| 106 <param name="refgen_version" ftype="text" value="GRCh37" /> | |
| 107 <output name="outfile"> | |
| 108 <assert_contents> | |
| 109 <has_size value= "659" delta="100" /> | |
| 110 </assert_contents> | |
| 111 </output> | |
| 112 </test> | |
| 113 <!-- Test 2 - Trio --> | |
| 114 <test expect_num_outputs="1"> | |
| 115 <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/> | |
| 116 <param name="proband_bam" ftype="bam" value="proband.bam" /> | |
| 117 <param name="proband_sex" ftype="text" value="female" /> | |
| 118 <param name="proband_name" ftype="text" value="Case5C" /> | |
| 119 <param name="genes" ftype="text" value="BRCA1" /> | |
| 120 <param name="refgen_version" ftype="text" value="GRCh37" /> | |
| 121 <conditional name="input_type"> | |
| 122 <param name="input_type_selector" value="trio"/> | |
| 123 <section name="mother"> | |
| 124 <param name="vcf" ftype="vcf" value="family.vcf.gz"/> | |
| 125 <param name="bam" ftype="bam" value="mother.bam" /> | |
| 126 <param name="affected" ftype="text" value="affected" /> | |
| 127 <param name="name" ftype="text" value="Case5M" /> | |
| 128 </section> | |
| 129 <section name="father"> | |
| 130 <param name="vcf" ftype="vcf" value="family.vcf.gz"/> | |
| 131 <param name="bam" ftype="bam" value="father.bam" /> | |
| 132 <param name="affected" ftype="text" value="unaffected" /> | |
| 133 <param name="name" ftype="text" value="Case5F" /> | |
| 134 </section> | |
| 135 </conditional> | |
| 136 <output name="outfile"> | |
| 137 <assert_contents> | |
| 138 <has_size value= "1555" delta="500" /> | |
| 139 </assert_contents> | |
| 140 </output> | |
| 141 </test> | |
| 142 </tests> | |
| 143 <help><![CDATA[ | |
| 144 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. | |
| 145 | |
| 146 .. class:: Warning mark | |
| 147 | |
| 148 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. | |
| 149 | |
| 150 Required inputs: | |
| 151 | |
| 152 1. Proband VCF file | |
| 153 | |
| 154 Optional inputs (trio analysis): | |
| 155 | |
| 156 1. Proband BAM file | |
| 157 2. Father & Mother BAM file | |
| 158 3. Father & Mother VCF file | |
| 159 | |
| 160 The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_. | |
| 161 | |
| 162 .. _iobio project: https://iobio.io | |
| 163 .. _Marth lab: https://marthlab.org/ | |
| 164 .. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/ | |
| 165 ]]></help> | |
| 166 <citations> | |
| 167 <citation type="doi">10.1038/s41598-021-99752-5</citation> | |
| 168 </citations> | |
| 169 </tool> |