Mercurial > repos > jeremyjliu > region_motif_data_manager
comparison data_manager/data_manager_fetch_motifs.xml @ 0:cab6e1cb4c2a draft default tip
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| author | jeremyjliu |
|---|---|
| date | Sat, 16 May 2015 17:23:06 -0400 |
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| -1:000000000000 | 0:cab6e1cb4c2a |
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| 1 <tool id="data_manager_fetch_motifs" name="Install Motif Database" version="1.0.0" tool_type="manage_data"> | |
| 2 <description>Downloads motif databases in tabix format for use with region_motif_enrichment</description> | |
| 3 <command interpreter="python">data_manager_fetch_motifs.py "${out_file}" --motif_db ${motif_db_selector}</command> | |
| 4 <inputs> | |
| 5 <param name="motif_db_selector" type="select" label="Choose the source for the motif db"> | |
| 6 <option value="test" selected="True">Test Encode Motifs (hg19)</option> | |
| 7 <option value="encode">Encode Motifs (hg19)</option> | |
| 8 <option value="jaspar">Jaspar and Jolma Motifs (hg19)</option> | |
| 9 <option value="mouse">Mouse Motifs (mm9)</option> | |
| 10 </param> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data name="out_file" format="data_manager_json"/> | |
| 14 </outputs> | |
| 15 <help> | |
| 16 **What it does** | |
| 17 | |
| 18 Fetches a reference motif database (bgz and tbi files) from Harvard | |
| 19 CBMI source and populates the "motif_databases" data table. | |
| 20 | |
| 21 **TO DO** | |
| 22 | |
| 23 Ability to add motif database from local file, as the last step in | |
| 24 a MEME pipeline. | |
| 25 </help> | |
| 26 </tool> |