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1 <tool id="data_manager_snpsift_dbnsfp" name="SnpSift dbNSFP" version="4.1.0" tool_type="manage_data">
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2 <description>Install a dbNSFP variant annotation database</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.7">pysam</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 #import re
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8 data_manager_snpsift_dbnsfp.py
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9 #if $db.src == 'softgenetics':
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10 --softgenetics $db.softgenetics_name
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11 #elif $db.src == 'history':
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12 #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp':
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13 #import os.path
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14 --snpsiftdbnsfp $os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)
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15 #else
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16 --dbnsfp_tabular $db.snpsiftdbnsfp
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17 #end if
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18 --db_name $db.db_name
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19 #if str($db.dbkey).strip() != '':
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20 --dbkey "$db.dbkey"
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21 #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?':
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22 --dbkey "$db.snpsiftdbnsfp.metadata.dbkey"
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23 #end if
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24 #end if
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25 "$out_file"
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26 </command>
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27 <inputs>
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28 <conditional name="db">
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29 <param name="src" type="select" label="Source for dbNSFP file">
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30 <option value="softgenetics">Jpopgen dbNSFP from softgenetics</option>
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31 <option value="history">from your history</option>
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32 </param>
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33 <when value="softgenetics">
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34 <param name="softgenetics_name" type="text" value="" label="dbNSFP file name at softgenetics ftp site">
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35 <help>Download From: ftp://dbnsfp.softgenetics.com/
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36 Enter the name of the database, e.g.: dbNSFPv3.0c.zip
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37 </help>
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38 <validator type="regex" message="A dbNSFP or dbscSNV .zip">(dbNSFP|dbscSNV).*[.]zip</validator>
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39 </param>
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40 </when>
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41 <when value="history">
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42 <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history"
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43 help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/>
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44 <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database">
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45 <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/>
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46 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
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47 </param>
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48 <param name="dbkey" type="text" value="hg19" optional="true" label="DBKEY to assign to data to this dbNSFP database" />
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49 </when>
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50 </conditional>
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51 </inputs>
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52
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53 <outputs>
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54 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
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55 </outputs>
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56 <stdio>
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57 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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58 <exit_code range="1:" level="fatal" description="Error" />
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59 </stdio>
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60 <tests>
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61 <test>
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62 <param name="src" value="history"/>
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63 <param name="snpsiftdbnsfp" value="test_nsfp.tsv" ftype="dbnsfp.tabular"/>
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64 <param name="dbkey" value="hg19"/>
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65 <param name="db_name" value="test_nsfp_tsv" />
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66 <output name="out_file" file="test_nsfp.data_manager_json"/>
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67 </test>
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68 </tests>
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69 <help>
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70
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71 This tool installs dbNSFP_ databases to annotate VCF files using SnpSift_dbNSFP_
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72 It populates data table: snpsift_dbnsfps
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73
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74 .. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP
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75 .. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP
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76
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77 Please cite:
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78 "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]
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79
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80 </help>
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81 </tool>
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82
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