Mercurial > repos > iuc > geneiobio
annotate geneiobio-iframe.xml @ 1:fc53fcdbe548 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit fab39612473d91e048868d9c122d7dd61a2bd9d4
author | iuc |
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date | Mon, 24 Jul 2023 16:06:54 +0000 |
parents | c0af7b196a89 |
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rev | line source |
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1
fc53fcdbe548
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit fab39612473d91e048868d9c122d7dd61a2bd9d4
iuc
parents:
0
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changeset
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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
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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
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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
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4 <configfiles> |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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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
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6 <html> |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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7 <body> |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
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changeset
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8 <iframe src="https://gene.iobio.io/?genes=${genes} |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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9 &species=Human |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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10 &build=${refgen_version} |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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11 &affectedSibs= |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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12 &unaffectedSibs= |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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13 &rel0=proband |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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14 &sex0=${proband_sex} |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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15 &vcf0=${__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
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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:
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changeset
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17 #if $proband_bam.ext == 'bam': |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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18 &bam0=${__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
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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
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20 #elif $proband_bam.ext == 'cram': |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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21 &cram0=${__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
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22 &cai0=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($proband_bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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23 #end if |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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24 &sample0=${proband_name} |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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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
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26 #if str( $input_type.input_type_selector ) == "trio"# |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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27 &rel1=father |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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28 &sex1=male |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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29 &vcf1=${__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
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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
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31 #if $input_type.father.bam.ext == 'bam': |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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32 &bam1=${__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
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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
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34 #elif $input_type.father.bam.ext == 'cram': |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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35 &cram1=${__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
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36 &cai1=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.father.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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37 #end if |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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38 &sample1=${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
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39 &affectedStatus1=${input_type.father.affected} |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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40 &rel2=mother |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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41 &sex2=female |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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42 &vcf2=${__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
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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
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44 #if $input_type.mother.bam.ext == 'bam': |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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45 &bam2=${__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
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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
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47 #elif $input_type.mother.bam.ext == 'cram': |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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48 &cram2=${__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
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49 &cai2=${__app__.config.galaxy_infrastructure_url}/api/datasets/${__app__.security.encode_id($input_type.mother.bam.id)}/metadata_file%3Fmetadata_file%3Dcram_index |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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50 #end if |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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51 &sample2=${input_type.mother.name} |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
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changeset
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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:
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changeset
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53 #end if |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
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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
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55 </body></html> |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
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56 ]]></configfile> |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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57 </configfiles> |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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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
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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
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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
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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:
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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:
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changeset
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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
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64 </param> |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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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
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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
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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
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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
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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:
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changeset
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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
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71 </param> |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
diff
changeset
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72 <when value="trio"> |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
iuc
parents:
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changeset
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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
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74 <param name="vcf" type="data" format="vcf_bgzip" label="Father VCF file"/> |
0
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75 <param name="bam" type="data" format="bam,cram" label="Father BAM file" optional="true"/> |
c0af7b196a89
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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
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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
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78 </section> |
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79 <section name="mother" title="Mother input"> |
1
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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
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81 <param name="bam" type="data" format="bam,cram" label="Mother BAM file" optional="true"/> |
c0af7b196a89
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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
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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
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84 </section> |
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85 </when> |
c0af7b196a89
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86 <when value="single"> |
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87 </when> |
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88 </conditional> |
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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
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90 <param name="refgen_version" type="select" label="Select reference genome version"> |
c0af7b196a89
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91 <option value="GRCh38" selected="true">GRCh38</option> |
c0af7b196a89
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92 <option value="GRCh37">GRCh37</option> |
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93 </param> |
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94 </inputs> |
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95 <outputs> |
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96 <data name="outfile" format="html" /> |
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97 </outputs> |
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98 <tests> |
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99 <!-- Test 1 - Single --> |
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100 <test expect_num_outputs="1"> |
c0af7b196a89
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101 <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/> |
c0af7b196a89
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102 <param name="proband_bam" ftype="bam" value="proband.bam" /> |
c0af7b196a89
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103 <param name="proband_sex" ftype="text" value="female" /> |
c0af7b196a89
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104 <param name="proband_name" ftype="text" value="Case5C" /> |
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105 <param name="genes" ftype="text" value="BRCA1" /> |
c0af7b196a89
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106 <param name="refgen_version" ftype="text" value="GRCh37" /> |
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107 <output name="outfile"> |
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108 <assert_contents> |
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109 <has_size value= "659" delta="100" /> |
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110 </assert_contents> |
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111 </output> |
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112 </test> |
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113 <!-- Test 2 - Trio --> |
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114 <test expect_num_outputs="1"> |
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115 <param name="proband_vcf" ftype="vcf" value="family.vcf.gz"/> |
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116 <param name="proband_bam" ftype="bam" value="proband.bam" /> |
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117 <param name="proband_sex" ftype="text" value="female" /> |
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118 <param name="proband_name" ftype="text" value="Case5C" /> |
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119 <param name="genes" ftype="text" value="BRCA1" /> |
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120 <param name="refgen_version" ftype="text" value="GRCh37" /> |
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121 <conditional name="input_type"> |
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122 <param name="input_type_selector" value="trio"/> |
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123 <section name="mother"> |
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124 <param name="vcf" ftype="vcf" value="family.vcf.gz"/> |
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125 <param name="bam" ftype="bam" value="mother.bam" /> |
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126 <param name="affected" ftype="text" value="affected" /> |
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127 <param name="name" ftype="text" value="Case5M" /> |
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128 </section> |
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129 <section name="father"> |
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130 <param name="vcf" ftype="vcf" value="family.vcf.gz"/> |
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131 <param name="bam" ftype="bam" value="father.bam" /> |
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132 <param name="affected" ftype="text" value="unaffected" /> |
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133 <param name="name" ftype="text" value="Case5F" /> |
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134 </section> |
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135 </conditional> |
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136 <output name="outfile"> |
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137 <assert_contents> |
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138 <has_size value= "1555" delta="500" /> |
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139 </assert_contents> |
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140 </output> |
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141 </test> |
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142 </tests> |
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143 <help><![CDATA[ |
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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. |
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145 |
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146 .. class:: Warning mark |
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147 |
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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. |
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149 |
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150 Required inputs: |
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151 |
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152 1. Proband VCF file |
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153 |
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154 Optional inputs (trio analysis): |
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155 |
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156 1. Proband BAM file |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
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157 2. Father & Mother BAM file |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
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158 3. Father & Mother VCF file |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
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159 |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
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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
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161 |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
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162 .. _iobio project: https://iobio.io |
c0af7b196a89
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
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163 .. _Marth lab: https://marthlab.org/ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
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164 .. _University of Utah Center for Genetic Discovery: https://ucgd.genetics.utah.edu/ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/geneiobio commit b5dd06c260082585428de394111cba0872f0e608
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165 ]]></help> |
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166 <citations> |
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167 <citation type="doi">10.1038/s41598-021-99752-5</citation> |
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168 </citations> |
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169 </tool> |