| Next changeset 1:fc53fcdbe548 (2023-07-24) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608 |
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added:
geneiobio-iframe.xml test-data/family.vcf.gz test-data/father.bam test-data/mother.bam test-data/proband.bam |
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| diff -r 000000000000 -r c0af7b196a89 geneiobio-iframe.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/geneiobio-iframe.xml Thu Jun 29 08:33:46 2023 +0000 |
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| b'@@ -0,0 +1,169 @@\n+<tool id="gene_iobio_display_generation_iframe" name="gene.iobio visualisation" version="4.7.1">\n+\t<description>analyses VCFs for single and trio analysis to find causative variants using gene.iobio\'s public server</description>\n+\t<command>cat \'$index\' | tr -d \'\\n\' > \'$outfile\'</command>\n+\t<configfiles>\n+\t\t<configfile name="index"><![CDATA[\n+<html>\n+\t<body>\n+\t\t<iframe src="https://gene.iobio.io/?genes=${genes}\n+&species=Human\n+&build=${refgen_version}\n+&affectedSibs=\n+&unaffectedSibs=\n+&rel0=proband\n+&sex0=${proband_sex}\n+&vcf0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/display\n+&tbi0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index\n+#if $proband_bam.ext == \'bam\':\n+&bam0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display\n+&bai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index\n+#elif $proband_bam.ext == \'cram\':\n+&cram0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display\n+&cai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index\n+#end if\n+&sample0=${proband_name}\n+&affectedStatus0=${proband_affected}\n+#if str( $input_type.input_type_selector ) == "trio"#\n+&rel1=father\n+&sex1=male\n+&vcf1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/display\n+&tbi1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index\n+#if $input_type.father.bam.ext == \'bam\':\n+&bam1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display\n+&bai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index\n+#elif $input_type.father.bam.ext == \'cram\':\n+&cram1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display\n+&cai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index\n+#end if\n+&sample1=${input_type.father.name}\n+&affectedStatus1=${input_type.father.affected}\n+&rel2=mother\n+&sex2=female\n+&vcf2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/display\n+&tbi2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index\n+#if $input_type.mother.bam.ext == \'bam\':\n+&bam2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display\n+&bai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index\n+#elif $input_type.mother.bam.ext == \'cram\':\n+&cram2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display\n+&cai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index\n+#end if\n+&sample2=${input_type.mother.name}\n+&affectedStatus2=${input_type.mother.affected}\n+#end if\n+" style="width: 100%; height: 900px;"></iframe>\n+</body></html>\n+ ]]></configfile>\n+\t</configfiles>\n+ <inputs>\n+ <param name="proband_vcf" type="data" format="vcf,vcf_bgzip" label="Proband VCF file"/>\n+ <param name="proband_ba'..b'fected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the mother affected?"/>\n+ <param name="name" type="text" value="M" label="Mother sample name" help="The sample names are listed in the columns of the VCF."/>\n+ </section>\n+ </when>\n+\t\t\t<when value="single">\n+\t\t\t</when>\n+ </conditional>\n+ <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."/>\n+ <param name="refgen_version" type="select" label="Select reference genome version">\n+ <option value="GRCh38" selected="true">GRCh38</option>\n+ <option value="GRCh37">GRCh37</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="outfile" format="html" />\n+ </outputs>\n+ <tests>\n+\t <!-- Test 1 - Single -->\n+ <test expect_num_outputs="1"> \n+ <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/>\n+\t\t\t<param name="proband_bam" ftype="bam" value="proband.bam" />\n+\t\t\t<param name="proband_sex" ftype="text" value="female" />\n+\t\t\t<param name="proband_name" ftype="text" value="Case5C" />\n+\t\t\t<param name="genes" ftype="text" value="BRCA1" />\n+\t\t\t<param name="refgen_version" ftype="text" value="GRCh37" />\n+ <output name="outfile">\n+ <assert_contents>\n+ <has_size value= "659" delta="100" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <!-- Test 2 - Trio -->\n+ <test expect_num_outputs="1"> \n+ <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/>\n+\t\t\t<param name="proband_bam" ftype="bam" value="proband.bam" />\n+\t\t\t<param name="proband_sex" ftype="text" value="female" />\n+\t\t\t<param name="proband_name" ftype="text" value="Case5C" />\n+\t\t\t<param name="genes" ftype="text" value="BRCA1" />\n+\t\t\t<param name="refgen_version" ftype="text" value="GRCh37" />\n+\t\t\t<conditional name="input_type">\n+\t\t\t\t<param name="input_type_selector" value="trio"/>\n+\t\t\t\t<section name="mother">\n+\t\t\t\t\t<param name="vcf" ftype="vcf" value="family.vcf.gz"/>\n+\t\t\t\t\t<param name="bam" ftype="bam" value="mother.bam" />\n+\t\t\t\t\t<param name="affected" ftype="text" value="affected" />\n+\t\t\t\t\t<param name="name" ftype="text" value="Case5M" />\n+\t\t\t\t</section>\n+\t\t\t\t<section name="father">\n+\t\t\t\t\t<param name="vcf" ftype="vcf" value="family.vcf.gz"/>\n+\t\t\t\t\t<param name="bam" ftype="bam" value="father.bam" />\n+\t\t\t\t\t<param name="affected" ftype="text" value="unaffected" />\n+\t\t\t\t\t<param name="name" ftype="text" value="Case5F" />\n+\t\t\t\t</section>\n+ </conditional>\n+ <output name="outfile">\n+ <assert_contents>\n+ <has_size value= "1555" delta="500" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ 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.\n+\t\n+\t.. class:: Warning mark\n+\n+\tThis 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.\n+\t\n+ Required inputs:\n+\n+ 1. Proband VCF file\n+\n+ Optional inputs (trio analysis):\n+\n+ 1. Proband BAM file\n+ 2. Father & Mother BAM file\n+ 3. Father & Mother VCF file\n+\n+ The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_.\n+\n+ .. _iobio project: https://iobio.io\n+ .. _Marth lab: https://marthlab.org/\n+ .. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/\n+ ]]></help>\n+\t<citations>\n+\t\t<citation type="doi">10.1038/s41598-021-99752-5</citation>\n+\t</citations>\n+</tool>\n' |
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| diff -r 000000000000 -r c0af7b196a89 test-data/family.vcf.gz |
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| diff -r 000000000000 -r c0af7b196a89 test-data/father.bam |
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| diff -r 000000000000 -r c0af7b196a89 test-data/mother.bam |
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| diff -r 000000000000 -r c0af7b196a89 test-data/proband.bam |
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| Binary file test-data/proband.bam has changed |