Mercurial > repos > jjohnson > data_manager_snpsift_dbnsfp
diff data_manager/data_manager_snpsift_dbnsfp.xml @ 0:da5d5dc2e55c draft default tip
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| author | jjohnson |
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| date | Wed, 09 Dec 2015 13:58:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_snpsift_dbnsfp.xml Wed Dec 09 13:58:01 2015 -0500 @@ -0,0 +1,82 @@ +<tool id="data_manager_snpsift_dbnsfp" name="SnpSift dbNSFP" version="4.1.0" tool_type="manage_data"> + <description>Install a dbNSFP variant annotation database</description> + <requirements> + <requirement type="package" version="0.7.7">pysam</requirement> + </requirements> + <command interpreter="python"> + #import re + data_manager_snpsift_dbnsfp.py + #if $db.src == 'softgenetics': + --softgenetics $db.softgenetics_name + #elif $db.src == 'history': + #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp': + #import os.path + --snpsiftdbnsfp $os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip) + #else + --dbnsfp_tabular $db.snpsiftdbnsfp + #end if + --db_name $db.db_name + #if str($db.dbkey).strip() != '': + --dbkey "$db.dbkey" + #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?': + --dbkey "$db.snpsiftdbnsfp.metadata.dbkey" + #end if + #end if + "$out_file" + </command> + <inputs> + <conditional name="db"> + <param name="src" type="select" label="Source for dbNSFP file"> + <option value="softgenetics">Jpopgen dbNSFP from softgenetics</option> + <option value="history">from your history</option> + </param> + <when value="softgenetics"> + <param name="softgenetics_name" type="text" value="" label="dbNSFP file name at softgenetics ftp site"> + <help>Download From: ftp://dbnsfp.softgenetics.com/ + Enter the name of the database, e.g.: dbNSFPv3.0c.zip + </help> + <validator type="regex" message="A dbNSFP or dbscSNV .zip">(dbNSFP|dbscSNV).*[.]zip</validator> + </param> + </when> + <when value="history"> + <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history" + help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/> + <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database"> + <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/> + <validator type="regex" message="No whitespace allowed">^\S*$</validator> + </param> + <param name="dbkey" type="text" value="hg19" optional="true" label="DBKEY to assign to data to this dbNSFP database" /> + </when> + </conditional> + </inputs> + + <outputs> + <data name="out_file" format="data_manager_json" label="${tool.name}"/> + </outputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <tests> + <test> + <param name="src" value="history"/> + <param name="snpsiftdbnsfp" value="test_nsfp.tsv" ftype="dbnsfp.tabular"/> + <param name="dbkey" value="hg19"/> + <param name="db_name" value="test_nsfp_tsv" /> + <output name="out_file" file="test_nsfp.data_manager_json"/> + </test> + </tests> + <help> + +This tool installs dbNSFP_ databases to annotate VCF files using SnpSift_dbNSFP_ +It populates data table: snpsift_dbnsfps + +.. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP +.. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP + +Please cite: +"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process] + + </help> +</tool> +