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Create an example blastdb Data Manager.
author Daniel Blankenberg <dan@bx.psu.edu>
date Wed, 11 Dec 2013 16:24:11 -0500
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1 <tool id="data_manager_blast_db" name="Blast DB" version="0.0.1" tool_type="manage_data">
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2 <description>Downloader</description>
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3 <command interpreter="python">fetch_blast_db.py --filename "${out_file}" --tool_data_table_name "blastdb"</command>
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4 <requirements>
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5 <requirement type="package" version="2.2.28">blast+</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Tool exception" />
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9 </stdio>
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10 <inputs>
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11 <param name="blastdb_name" type="text" label="Blast DB Name" help="try &quot;nt&quot; as an example" optional="False"/>
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12 <conditional name="advanced">
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13 <param name="advanced_selector" type="select" label="Advanced Options">
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14 <option value="basic" selected="True">Basic</option>
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15 <option value="advanced">Advanced</option>
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16 </param>
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17 <when value="basic">
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18 </when>
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19 <when value="advanced">
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20 <param type="text" name="data_description" value="" label="Display name" help="Optional"/>
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21 <param type="text" name="data_id" value="" label="ID for sequence" help="Optional"/>
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22 </when>
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23 </conditional>
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24 </inputs>
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25 <outputs>
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26 <data name="out_file" format="data_manager_json"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="blastdb_name" value="est"/>
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31 <param name="advanced_selector" value="basic"/>
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32 <output name="out_file" file="est_out.json"/>
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33 </test>
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34 </tests>
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35 <help>
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36 **What it does**
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37
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38 Downloads Blast DBs and updates blastdb tool data tables.
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39
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40 ------
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41
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42
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43 .. class:: infomark
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44
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45 **Notice:** This is a functional, but basic, tool for fetching preformatted blastdbs.
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46
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47 </help>
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48 </tool>