Mercurial > repos > jjohnson > snpeff
annotate data_manager/data_manager_snpEff_download.xml @ 7:0ad9733e22a4
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 29 Nov 2013 09:27:22 -0500 |
| parents | eb394dd65c98 |
| children |
| rev | line source |
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5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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1 <tool id="data_manager_snpeff_download" name="SnpEff Download" version="3.4" tool_type="manage_data"> |
| 0 | 2 <description>Download a new database</description> |
| 3 <requirements> | |
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5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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4 <requirement type="package" version="3.4">snpEff</requirement> |
| 0 | 5 </requirements> |
| 6 <command interpreter="python"> | |
| 2 | 7 data_manager_snpEff_download.py --jar_path \$SNPEFF_JAR_PATH/snpEff.jar --config \$SNPEFF_JAR_PATH/snpEff.config |
| 0 | 8 --genome_version "${genome_databases.fields.value}" |
| 9 --organism "${genome_databases.fields.name}" | |
| 10 "$out_file" | |
| 11 </command> | |
| 12 <inputs> | |
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6
eb394dd65c98
Add mutli-select to data managers from Bjoern, filter unique database options in snpEff_download.xml snpEff.xml
Jim Johnson <jj@umn.edu>
parents:
5
diff
changeset
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13 <param name="genome_databases" type="select" display="checkboxes" multiple="true" label="Genome Version"> |
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5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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14 <options from_data_table="snpeff_databases"> |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
15 <filter type="sort_by" column="0" /> |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
16 </options> |
| 0 | 17 </param> |
| 18 </inputs> | |
| 19 | |
| 20 <outputs> | |
| 21 <data name="out_file" format="data_manager_json" label="${tool.name} : ${genome_databases.fields.value}"/> | |
| 22 </outputs> | |
| 23 <stdio> | |
| 24 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 25 <exit_code range="1:" level="fatal" description="Error" /> | |
| 26 </stdio> | |
| 4 | 27 <tests> |
| 28 <test> | |
| 29 <param name="genome_databases" value="GRCh37.71"/> | |
| 30 <output name="out_file"> | |
| 31 <assert_contents> | |
| 32 <!-- Check that a genome was added --> | |
| 33 <has_text text="GRCh37.71" /> | |
| 34 <has_text text="snpeff_regulationdb" /> | |
| 35 <has_text text="snpeff_annotations" /> | |
| 36 </assert_contents> | |
| 37 </output> | |
| 38 </test> | |
| 39 </tests> | |
| 0 | 40 <help> |
| 41 | |
| 42 This tool downloads a SnpEff database. | |
| 43 | |
| 44 For details about this tool, please go to http://snpEff.sourceforge.net | |
| 45 | |
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5
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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46 Please cite: |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
47 "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] |
|
8952990fcab9
Update to snpEff version 3.4 and add data managers to download snpEff genome reference databases
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
|
48 |
| 0 | 49 </help> |
| 50 </tool> | |
| 51 |