Mercurial > repos > jjohnson > data_manager_snpeff
annotate data_manager/data_manager_snpEff_download.xml @ 3:c6769a700e55
Update loc data to separate version 4 databases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 21 Oct 2014 14:04:33 -0500 |
| parents | 8ac7bbaac976 |
| children | 6a378d0f4856 |
| rev | line source |
|---|---|
| 1 | 1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.0" tool_type="manage_data"> |
| 0 | 2 <description>Download a new database</description> |
| 3 <requirements> | |
| 1 | 4 <requirement type="package" version="4.0">snpEff</requirement> |
| 0 | 5 </requirements> |
| 6 <command interpreter="python"> | |
| 7 data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config | |
| 8 #if $snpDb.genomeSrc == "named": | |
| 9 --genome_version "${snpDb.genome_version}" | |
| 10 #else | |
| 11 --genome_version "${snpDb.genome_databases.fields.value}" | |
| 12 --organism "${snpDb.genome_databases.fields.name}" | |
| 13 #end if | |
| 14 "$out_file" | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <conditional name="snpDb"> | |
| 18 <param name="genomeSrc" type="select" label="Select Genome Version"> | |
| 19 <help>The list is very large and may take some time to display on your browser</help> | |
| 20 <option value="named">By Genome Version Name</option> | |
| 21 <option value="cached">Select from list</option> | |
| 22 </param> | |
| 23 <when value="named"> | |
| 24 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh37.74)"> | |
| 25 <help>http://sourceforge.net/projects/snpeff/files/databases/</help> | |
| 26 <validator type="regex" message="A genome version name is required">\S+</validator> | |
| 27 </param> | |
| 28 </when> | |
| 29 <when value="cached"> | |
| 30 <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version"> | |
|
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c6769a700e55
Update loc data to separate version 4 databases
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
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31 <options from_data_table="snpeff4_databases"> |
| 0 | 32 <filter type="sort_by" column="0" /> |
| 33 </options> | |
| 34 </param> | |
| 35 </when> | |
| 36 </conditional> | |
| 37 </inputs> | |
| 38 | |
| 39 <outputs> | |
| 40 <data name="out_file" format="data_manager_json" label="${tool.name}"/> | |
| 41 </outputs> | |
| 42 <stdio> | |
| 43 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 44 <exit_code range="1:" level="fatal" description="Error" /> | |
| 45 </stdio> | |
| 46 <tests> | |
| 47 <test> | |
| 48 <param name="genomeSrc" value="named"/> | |
|
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c6769a700e55
Update loc data to separate version 4 databases
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
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49 <param name="genome_version" value="GRCh38.76"/> |
| 0 | 50 <output name="out_file"> |
| 51 <assert_contents> | |
| 52 <!-- Check that a genome was added --> | |
|
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c6769a700e55
Update loc data to separate version 4 databases
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
53 <has_text text="GRCh38.76" /> |
|
c6769a700e55
Update loc data to separate version 4 databases
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
54 <has_text text="snpeff4_regulationdb" /> |
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c6769a700e55
Update loc data to separate version 4 databases
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
55 <has_text text="snpeff4_annotations" /> |
| 0 | 56 </assert_contents> |
| 57 </output> | |
| 58 </test> | |
| 59 </tests> | |
| 60 <help> | |
| 61 | |
| 62 This tool downloads a SnpEff database. | |
| 63 | |
| 64 For details about this tool, please go to http://snpEff.sourceforge.net | |
| 65 | |
| 66 Please cite: | |
| 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] | |
| 68 | |
| 69 </help> | |
| 70 </tool> | |
| 71 |