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