Mercurial > repos > jjohnson > data_manager_snpeff
annotate data_manager/data_manager_snpEff_download.xml @ 5:78bcf4ac437c
Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 13 Jan 2015 12:54:20 -0600 |
| parents | 6a378d0f4856 |
| children | a329eda0cdff |
| 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 | |
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8 --genome_version "$genome_version" "$out_file" |
| 0 | 9 </command> |
| 10 <inputs> | |
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11 <param name="genome_version" type="text" size="40" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> |
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12 <help>http://sourceforge.net/projects/snpeff/files/databases/</help> |
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parents:
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13 <validator type="regex" message="A genome version name is required">\S+</validator> |
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Only download by name, available genome list now too large to be practical
Jim Johnson <jj@umn.edu>
parents:
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14 </param> |
| 0 | 15 </inputs> |
| 16 | |
| 17 <outputs> | |
| 18 <data name="out_file" format="data_manager_json" label="${tool.name}"/> | |
| 19 </outputs> | |
| 20 <stdio> | |
| 21 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> | |
| 22 <exit_code range="1:" level="fatal" description="Error" /> | |
| 23 </stdio> | |
| 24 <tests> | |
| 25 <test> | |
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Jim Johnson <jj@umn.edu>
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26 <param name="genome_version" value="GRCh38.76"/> |
| 0 | 27 <output name="out_file"> |
| 28 <assert_contents> | |
| 29 <!-- Check that a genome was added --> | |
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parents:
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30 <has_text text="GRCh38.76" /> |
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78bcf4ac437c
Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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31 <has_text text="snpeffv_regulationdb" /> |
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78bcf4ac437c
Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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32 <has_text text="snpeffv_annotations" /> |
| 0 | 33 </assert_contents> |
| 34 </output> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 | |
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78bcf4ac437c
Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
Jim Johnson <jj@umn.edu>
parents:
4
diff
changeset
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39 This tool downloads a SnpEff database and populates data tables: snpeffv_genomedb, snpeffv_regulationdb, and snpeffv_annotations. |
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6a378d0f4856
Only download by name, available genome list now too large to be practical
Jim Johnson <jj@umn.edu>
parents:
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changeset
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40 |
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6a378d0f4856
Only download by name, available genome list now too large to be practical
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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41 To see the list of available SnpEff genomes run the "SnpEff Databases" data manager which records the available genome databases in data table: snpeff4_databases |
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6a378d0f4856
Only download by name, available genome list now too large to be practical
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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42 |
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6a378d0f4856
Only download by name, available genome list now too large to be practical
Jim Johnson <jj@umn.edu>
parents:
3
diff
changeset
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43 The SnpEff genome databases are at: http://sourceforge.net/projects/snpeff/files/databases/ |
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6a378d0f4856
Only download by name, available genome list now too large to be practical
Jim Johnson <jj@umn.edu>
parents:
3
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changeset
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44 |
| 0 | 45 |
| 46 For details about this tool, please go to http://snpEff.sourceforge.net | |
| 47 | |
| 48 Please cite: | |
| 49 "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] | |
| 50 | |
| 51 </help> | |
| 52 </tool> | |
| 53 |