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1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.0" tool_type="manage_data">
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2 <description>Download a new database</description>
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3 <requirements>
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4 <requirement type="package" version="4.0">snpEff</requirement>
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5 </requirements>
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6 <command interpreter="python">
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7 data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config
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8 #if $snpDb.genomeSrc == "named":
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9 --genome_version "${snpDb.genome_version}"
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10 #else
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11 --genome_version "${snpDb.genome_databases.fields.value}"
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12 --organism "${snpDb.genome_databases.fields.name}"
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13 #end if
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14 "$out_file"
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15 </command>
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16 <inputs>
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17 <conditional name="snpDb">
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18 <param name="genomeSrc" type="select" label="Select Genome Version">
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19 <help>The list is very large and may take some time to display on your browser</help>
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20 <option value="named">By Genome Version Name</option>
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21 <option value="cached">Select from list</option>
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22 </param>
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23 <when value="named">
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24 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)">
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25 <help>http://sourceforge.net/projects/snpeff/files/databases/</help>
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26 <validator type="regex" message="A genome version name is required">\S+</validator>
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27 </param>
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28 </when>
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29 <when value="cached">
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30 <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version">
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31 <options from_data_table="snpeff_databases">
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32 <filter type="sort_by" column="0" />
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33 </options>
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34 </param>
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35 </when>
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36 </conditional>
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37 </inputs>
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38
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39 <outputs>
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40 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
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41 </outputs>
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42 <stdio>
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43 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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44 <exit_code range="1:" level="fatal" description="Error" />
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45 </stdio>
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46 <tests>
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47 <test>
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48 <param name="genomeSrc" value="named"/>
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49 <param name="genome_version" value="GRCh37.71"/>
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50 <output name="out_file">
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51 <assert_contents>
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52 <!-- Check that a genome was added -->
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53 <has_text text="GRCh37.71" />
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54 <has_text text="snpeff_regulationdb" />
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55 <has_text text="snpeff_annotations" />
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60 <help>
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61
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62 This tool downloads a SnpEff database.
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63
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64 For details about this tool, please go to http://snpEff.sourceforge.net
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65
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66 Please cite:
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67 "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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68
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69 </help>
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70 </tool>
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71
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