Mercurial > repos > iuc > geneiobio

annotate geneiobio-iframe.xml @ 1:fc53fcdbe548 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit fab39612473d91e048868d9c122d7dd61a2bd9d4
author iuc
date Mon, 24 Jul 2023 16:06:54 +0000
parents c0af7b196a89
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
fc53fcdbe548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit fab39612473d91e048868d9c122d7dd61a2bd9d4
iuc
parents: 0
diff changeset
1 <tool id="gene_iobio_display_generation_iframe" name="gene.iobio visualisation" version="4.7.1+galaxy1">
0
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
2 <description>analyses VCFs for single and trio analysis to find causative variants using gene.iobio's public server</description>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
3 <command>cat '$index' | tr -d '\n' > '$outfile'</command>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
4 <configfiles>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
5 <configfile name="index"><![CDATA[
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
6 <html>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
7 <body>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
8 <iframe src="https://gene.iobio.io/?genes=${genes}
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
9 &species=Human
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
10 &build=${refgen_version}
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
11 &affectedSibs=
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
12 &unaffectedSibs=
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
13 &rel0=proband
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
14 &sex0=${proband_sex}
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
15 &vcf0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/display
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
16 &tbi0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
17 #if $proband_bam.ext == 'bam':
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
18 &bam0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
19 &bai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
20 #elif $proband_bam.ext == 'cram':
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
21 &cram0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/display
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
22 &cai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
23 #end if
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
24 &sample0=${proband_name}
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
25 &affectedStatus0=${proband_affected}
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
26 #if str( $input_type.input_type_selector ) == "trio"#
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
27 &rel1=father
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
28 &sex1=male
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
29 &vcf1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/display
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
30 &tbi1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
31 #if $input_type.father.bam.ext == 'bam':
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
32 &bam1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
33 &bai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
34 #elif $input_type.father.bam.ext == 'cram':
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
35 &cram1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/display
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
36 &cai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
37 #end if
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
38 &sample1=${input_type.father.name}
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
39 &affectedStatus1=${input_type.father.affected}
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
40 &rel2=mother
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
41 &sex2=female
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
42 &vcf2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/display
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
43 &tbi2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.vcf.id)}/metadata_file%3Fmetadata_file%3Dtabix_index
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
44 #if $input_type.mother.bam.ext == 'bam':
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
45 &bam2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
46 &bai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dbam_index
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
47 #elif $input_type.mother.bam.ext == 'cram':
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
48 &cram2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/display
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
49 &cai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
50 #end if
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
51 &sample2=${input_type.mother.name}
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
52 &affectedStatus2=${input_type.mother.affected}
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
53 #end if
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
54 " style="width: 100%; height: 900px;"></iframe>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
55 </body></html>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
56 ]]></configfile>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
57 </configfiles>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
58 <inputs>
1
fc53fcdbe548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit fab39612473d91e048868d9c122d7dd61a2bd9d4
iuc
parents: 0
diff changeset
59 <param name="proband_vcf" type="data" format="vcf_bgzip" label="Proband VCF file"/>
0
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
60 <param name="proband_bam" type="data" format="bam,cram" label="Proband BAM file" optional="true"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
61 <param name="proband_sex" type="select" display="radio" label="Proband sex">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
62 <option value="male" selected="true">Male</option>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
63 <option value="female">Female</option>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
64 </param>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
65 <param name="proband_affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="true" label="Is the proband affected?"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
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."/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
67 <conditional name="input_type">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
68 <param name="input_type_selector" type="select" display="radio" label="Single/Trio analysis">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
69 <option value="single" selected="true">Single</option>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
70 <option value="trio">Trio</option>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
71 </param>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
72 <when value="trio">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
73 <section name="father" title="Father input">
1
fc53fcdbe548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit fab39612473d91e048868d9c122d7dd61a2bd9d4
iuc
parents: 0
diff changeset
74 <param name="vcf" type="data" format="vcf_bgzip" label="Father VCF file"/>
0
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
75 <param name="bam" type="data" format="bam,cram" label="Father BAM file" optional="true"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
76 <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the father affected?"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
77 <param name="name" type="text" value="F" label="Father sample name" help="The sample names are listed in the columns of the VCF."/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
78 </section>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
79 <section name="mother" title="Mother input">
1
fc53fcdbe548 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit fab39612473d91e048868d9c122d7dd61a2bd9d4
iuc
parents: 0
diff changeset
80 <param name="vcf" type="data" format="vcf_bgzip" label="Mother VCF file"/>
0
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
81 <param name="bam" type="data" format="bam,cram" label="Mother BAM file" optional="true"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
82 <param name="affected" type="boolean" truevalue="affected" falsevalue="unaffected" checked="false" label="Is the mother affected?"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
83 <param name="name" type="text" value="M" label="Mother sample name" help="The sample names are listed in the columns of the VCF."/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
84 </section>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
85 </when>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
86 <when value="single">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
87 </when>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
88 </conditional>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
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."/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
90 <param name="refgen_version" type="select" label="Select reference genome version">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
91 <option value="GRCh38" selected="true">GRCh38</option>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
92 <option value="GRCh37">GRCh37</option>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
93 </param>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
94 </inputs>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
95 <outputs>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
96 <data name="outfile" format="html" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
97 </outputs>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
98 <tests>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
99 <!-- Test 1 - Single -->
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
100 <test expect_num_outputs="1">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
101 <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
102 <param name="proband_bam" ftype="bam" value="proband.bam" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
103 <param name="proband_sex" ftype="text" value="female" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
104 <param name="proband_name" ftype="text" value="Case5C" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
105 <param name="genes" ftype="text" value="BRCA1" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
106 <param name="refgen_version" ftype="text" value="GRCh37" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
107 <output name="outfile">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
108 <assert_contents>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
109 <has_size value= "659" delta="100" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
110 </assert_contents>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
111 </output>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
112 </test>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
113 <!-- Test 2 - Trio -->
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
114 <test expect_num_outputs="1">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
115 <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
116 <param name="proband_bam" ftype="bam" value="proband.bam" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
117 <param name="proband_sex" ftype="text" value="female" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
118 <param name="proband_name" ftype="text" value="Case5C" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
119 <param name="genes" ftype="text" value="BRCA1" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
120 <param name="refgen_version" ftype="text" value="GRCh37" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
121 <conditional name="input_type">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
122 <param name="input_type_selector" value="trio"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
123 <section name="mother">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
124 <param name="vcf" ftype="vcf" value="family.vcf.gz"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
125 <param name="bam" ftype="bam" value="mother.bam" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
126 <param name="affected" ftype="text" value="affected" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
127 <param name="name" ftype="text" value="Case5M" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
128 </section>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
129 <section name="father">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
130 <param name="vcf" ftype="vcf" value="family.vcf.gz"/>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
131 <param name="bam" ftype="bam" value="father.bam" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
132 <param name="affected" ftype="text" value="unaffected" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
133 <param name="name" ftype="text" value="Case5F" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
134 </section>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
135 </conditional>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
136 <output name="outfile">
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
137 <assert_contents>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
138 <has_size value= "1555" delta="500" />
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
139 </assert_contents>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
140 </output>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
141 </test>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
142 </tests>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
143 <help><![CDATA[
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
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.
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
145
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
146 .. class:: Warning mark
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
147
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
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.
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
149
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
150 Required inputs:
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
151
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
152 1. Proband VCF file
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
153
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
154 Optional inputs (trio analysis):
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
155
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
156 1. Proband BAM file
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
157 2. Father & Mother BAM file
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
158 3. Father & Mother VCF file
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
159
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
160 The `iobio project`_ is developed by the `Marth lab`_ at the `University of Utah Center for Genetic Discovery`_.
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
161
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
162 .. _iobio project: https://iobio.io
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
163 .. _Marth lab: https://marthlab.org/
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
164 .. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
165 ]]></help>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
166 <citations>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
167 <citation type="doi">10.1038/s41598-021-99752-5</citation>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
168 </citations>
c0af7b196a89 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff changeset
169 </tool>