|
0
|
1 <?xml version="1.0"?>
|
|
|
2
|
|
|
3 <tool id="hgvs_annotation_1" name="Functionally 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
|
|
|
12 <description>with deleterious change prediction, gene names, pathways, etc.</description>
|
|
|
13 <version_string>hgvs_table_annotate -v</version_string>
|
|
|
14 <command interpreter="perl">hgvs_table_annotate $__tool_data_path__ -q sift/$sift_dir polyphen2/$polyphen_file\.txt.gz gerp/$gerp_dir TissueDistributionDBs/$tissue_dist_file\.tab pathways/$pathways_file\.txt $refFlat_bed $input_hgvs_table $out_hgvs_annotated_table $keep_synonymous</command>
|
|
|
15 <inputs>
|
|
|
16 <param format="achri_snp_table" name="input_hgvs_table" type="data" label="Variant calls table with HGVS syntax"/>
|
|
|
17 <param name="keep_synonymous" type="boolean" label="Report synonymous variants?" default="false" truevalue="true" falsevalue="false"/>
|
|
|
18 <param name="sift_dir" type="select" display="radio" dynamic_options="SIFT_fileOptions()" label="SIFT precalculated tables" help="SIFT scores below 0.05 generally indicate a harmful variant"/>
|
|
|
19 <param name="polyphen_file" type="select" display="radio" dynamic_options="PolyPhen_fileOptions()" label="PolyPhen2 precalculated tables" help="Makes a call of deleterious, possibly deleterious, or benign"/>
|
|
|
20 <param name="gerp_dir" type="select" display="radio" dynamic_options="GERP_fileOptions()" label="GERP precalculated tables" help="GERP scores far from zero generally indicate a harmful variant"/>
|
|
|
21 <param name="tissue_dist_file" type="select" display="radio" dynamic_options="TissueDist_fileOptions()" label="Gene tissue distribution DB" help="Lists in descending order the major tissue types in which each gene is expressed"/>
|
|
|
22 <!--<param name="pseudogene_file" type="select" display="radio" dynamic_options="Pseudogene_fileOptions()" label="Pseudogene DB" help="Genes with pseudogenes are more likely to generate variant false positives through mismapping"/>-->
|
|
|
23 <param name="pathways_file" type="select" display="radio" dynamic_options="Pathway_fileOptions()" label="Biochemical Pathway DB" help="Gives an idea of processes in which the gene is involved"/>
|
|
|
24 <param name="refFlat_bed" type="data" format="bed" label="Gene Names DB" help="Import a refFlat file from the 'Genomic coding sequence regions' folder under Shared Data. Alternatively, provide a BED format file which defined exons and has the gene name in the 4th column"/>
|
|
|
25 </inputs>
|
|
|
26 <outputs>
|
|
|
27 <data format="achri_annotated_snp_table" name="out_hgvs_annotated_table" type="data" label="Functionally annotated HGVS variant table"/>
|
|
|
28 </outputs>
|
|
|
29
|
|
|
30 <!-- the following code populates the dbSNP selection from the public dbSNP datasets available in the local Galaxy installation -->
|
|
|
31 <code file="sift_datasets.py"/>
|
|
|
32 <code file="polyphen_datasets.py"/>
|
|
|
33 <code file="gerp_datasets.py"/>
|
|
|
34 <code file="tissuedist_datasets.py"/>
|
|
|
35 <!-- <code file="pseudogene_datasets.py"/>-->
|
|
|
36 <code file="pathways_datasets.py"/>
|
|
|
37
|
|
|
38 <tests>
|
|
|
39 </tests>
|
|
|
40
|
|
|
41 <help>
|
|
|
42 This tool reports several functional attributes, and potential for functional disturbance, based on genes that have declared sequence variants.
|
|
|
43 These results can be used to help find the genetic cause of a clinical phenotype.
|
|
|
44 </help>
|
|
|
45
|
|
|
46 </tool>
|
