Mercurial > repos > yusuf > annotate_hgvs

annotate AnnotateVariants.xml @ 0:9977d1935a07 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
initial commit
author Yusuf Ali <ali@yusuf.email>
date Wed, 25 Mar 2015 13:10:47 -0600
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
1 <?xml version="1.0"?>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
2
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
3 <tool id="hgvs_annotation_2" name="Annotate an HGVS table">
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
4 <requirements>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
5 <requirement type="package">genesplicer</requirement>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
6 <requirement type="package">human</requirement>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
7 <requirement type="package">score3.pl</requirement>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
8 <requirement type="package">score5.pl</requirement>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
9 </requirements>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
10
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
11 <description>with deleterious AA and splicing change predictions, protein domain disruptions, etc.</description>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
12 <version_string>hgvs_table_annotate -v</version_string>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
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>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
14 <inputs>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
15 <param format="achri_snp_table" name="input_hgvs_table" type="data" label="Variant calls table with HGVS syntax"/>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
16 </inputs>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
17 <outputs>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
18 <data format="achri_annotated_snp_table" name="out_hgvs_annotated_table" type="data" label="Functionally annotated HGVS variant table"/>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
19 </outputs>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
20
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
21 <tests>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
22 </tests>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
23
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
24 <help>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
25 This tool reports several functional attributes, and potential for functional disturbance, based on genes that have declared sequence variants.
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
26 These results can be used to help find the genetic cause of a clinical phenotype.
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
27 </help>
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
28
9977d1935a07 initial commit
Yusuf Ali <ali@yusuf.email>
parents:
diff changeset
29 </tool>