Mercurial > repos > iuc > data_manager_snpsift_dbnsfp

annotate data_manager/data_manager_snpsift_dbnsfp.xml @ 7:8636c3740779 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit ad15c8e96a0633f1939266d63fd17978afa7d9b7
author iuc
date Thu, 09 Feb 2023 14:55:03 +0000
parents 0a68ef0303c5
children
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0a68ef0303c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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1 <tool id="data_manager_snpsift_dbnsfp" name="SnpSift dbNSFP" version="4.1.1" tool_type="manage_data" profile="19.05">
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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="0.8.3">pysam</requirement>
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0a68ef0303c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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5 <requirement type="package" version="2.7">python</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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9 <exit_code range="1:" level="fatal" description="Error" />
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10 </stdio>
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0a68ef0303c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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11 <command>
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12 #import re
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0a68ef0303c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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13 python '$__tool_directory__/data_manager_snpsift_dbnsfp.py'
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14 #if $db.src == 'softgenetics':
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15 --softgenetics "$db.softgenetics_name"
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16 #elif $db.src == 'history':
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17 #if $db.snpsiftdbnsfp.is_of_type('snpsiftdbnsfp'):
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18 #import os.path
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19 --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)"
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20 #else
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21 --dbnsfp_tabular "$db.snpsiftdbnsfp"
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22 #end if
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23 --db_name "$db.db_name"
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24 #if str($db.dbkey).strip() != '':
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25 --dbkey "$db.dbkey"
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26 #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?':
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27 --dbkey "$db.snpsiftdbnsfp.metadata.dbkey"
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28 #end if
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29 #end if
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30 "$out_file"
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31 </command>
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32 <inputs>
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33 <conditional name="db">
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34 <param name="src" type="select" label="Source for dbNSFP file">
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35 <option value="softgenetics">Jpopgen dbNSFP from softgenetics</option>
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36 <option value="history">from your history</option>
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37 </param>
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38 <when value="softgenetics">
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39 <param name="softgenetics_name" type="text" value="" label="dbNSFP file name at softgenetics ftp site">
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40 <help>Download From: ftp://dbnsfp.softgenetics.com/
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41 Enter the name of the database, e.g.: dbNSFPv3.0c.zip
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42 </help>
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43 <validator type="regex" message="A dbNSFP or dbscSNV .zip">(dbNSFP|dbscSNV).*[.]zip</validator>
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44 </param>
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45 </when>
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46 <when value="history">
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47 <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history"
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48 help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/>
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49 <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database">
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50 <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/>
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51 <validator type="regex" message="No whitespace allowed">^\S*$</validator>
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52 </param>
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53 <param name="dbkey" type="text" value="hg19" optional="true" label="DBKEY to assign to data to this dbNSFP database" />
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54 </when>
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55 </conditional>
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56 </inputs>
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57
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58 <outputs>
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59 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="src" value="history"/>
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64 <param name="snpsiftdbnsfp" value="test_nsfp.tsv" ftype="dbnsfp.tabular"/>
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65 <param name="dbkey" value="hg19"/>
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66 <param name="db_name" value="test_nsfp_tsv" />
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67 <output name="out_file" file="test_nsfp.data_manager_json"/>
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68 </test>
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69 </tests>
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70 <help>
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71
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72 This tool installs dbNSFP_ databases to annotate VCF files using SnpSift_dbNSFP_
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73 It populates data table: snpsift_dbnsfps
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74
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75 .. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP
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76 .. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP
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5f429f5faba5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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78 Please refer to https://sites.google.com/site/jpopgen/dbNSFP for which citations to use with specific dbNSFP database versions.
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5f429f5faba5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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80 </help>
5f429f5faba5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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81 <citations>
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82 <citation type="doi">DOI: 10.1002/humu.21517</citation>
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83 <citation type="doi">DOI: 10.1002/humu.22376</citation>
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84 <citation type="doi">DOI: 10.1002/humu.22932</citation>
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85 <citation type="doi">doi: 10.1093/hmg/ddu733</citation>
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86 <citation type="doi">doi: 10.1093/nar/gku1206</citation>
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87 <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>
5f429f5faba5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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88 </citations>
5f429f5faba5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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89 </tool>
5f429f5faba5 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4
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90