Mercurial > repos > yusuf > annotate_hgvs
comparison AnnotateVariants.xml @ 0:9977d1935a07 default tip
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| author | Yusuf Ali <ali@yusuf.email> |
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| date | Wed, 25 Mar 2015 13:10:47 -0600 |
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| -1:000000000000 | 0:9977d1935a07 |
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| 1 <?xml version="1.0"?> | |
| 2 | |
| 3 <tool id="hgvs_annotation_2" name="Annotate an HGVS table"> | |
| 4 <requirements> | |
| 5 <requirement type="package">genesplicer</requirement> | |
| 6 <requirement type="package">human</requirement> | |
| 7 <requirement type="package">score3.pl</requirement> | |
| 8 <requirement type="package">score5.pl</requirement> | |
| 9 </requirements> | |
| 10 | |
| 11 <description>with deleterious AA and splicing change predictions, protein domain disruptions, etc.</description> | |
| 12 <version_string>hgvs_table_annotate -v</version_string> | |
| 13 <command interpreter="perl">hgvs_table_annotate $__tool_data_path__ -q /sift/hg19 /polyphen2/hg19.txt.gz /dbs/gerp/hg19 /dbs/TissueDistributionDBs/human.v2009-07-30.tab /dbs/pathways/KEGG.human.2012-09-25.txt /dbs/interpro_supermatch_hg19.bed /dbs/OMIM/morbidmap $input_hgvs_table $out_hgvs_annotated_table /hg19.fa</command> | |
| 14 <inputs> | |
| 15 <param format="achri_snp_table" name="input_hgvs_table" type="data" label="Variant calls table with HGVS syntax"/> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="achri_annotated_snp_table" name="out_hgvs_annotated_table" type="data" label="Functionally annotated HGVS variant table"/> | |
| 19 </outputs> | |
| 20 | |
| 21 <tests> | |
| 22 </tests> | |
| 23 | |
| 24 <help> | |
| 25 This tool reports several functional attributes, and potential for functional disturbance, based on genes that have declared sequence variants. | |
| 26 These results can be used to help find the genetic cause of a clinical phenotype. | |
| 27 </help> | |
| 28 | |
| 29 </tool> |