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author dchristiany
date Mon, 28 Oct 2019 06:53:13 -0400
parents 238a5328279d
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1 <tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.28.1" tool_type="manage_data">
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2 <requirements>
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3 </requirements>
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4 <stdio>
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5 <exit_code range="1:" />
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6 </stdio>
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7 <command><![CDATA[
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8 python $__tool_directory__/FROGS_data_manager.py
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9 --database="$database.database"
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10 #if $database.database=="frogs_db_data"
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11 --all_dbs="$database.db_type.db"
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12 #if $database.db_type.db=="false"
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13 --date="$database.db_type.date"
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14 --amplicons="$database.db_type.amplicons"
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15 --bases="$database.db_type.bases"
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16 --filters="$database.db_type.filters"
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17 #end if
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18 --only_last_versions="$database.only_last_versions"
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19 #end if
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20 --tool_data="$__tool_data_path__"
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21 --output "$output"
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22 ]]></command>
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23 <inputs>
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24 <conditional name="database">
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25 <param name="database" type="select" label="Please select a database to update">
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26 <option value="frogs_db_data">FROGS database (FROGS Affiliation OTU)</option>
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27 <option value="HVL_db_data">HVL database (FROGS Affiliation postprocess)</option>
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28 </param>
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29 <when value="frogs_db_data">
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30 <conditional name="db_type">
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31 <param name="db" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Download all databases"/>
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32 <when value="true"/>
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33 <when value="false">
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34 <param name="date" value="0" type="text" label="Only more recent database than this date will be downloaded" help="Please enter a date at the following format: YYYYMMDD, leave 0 for no date">
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35 <validator type="regex" message="Please enter a date at the following format: YYYYMMDD, leave 0 for no date">0|[1-2]{1}[0-9]{3}[0-1]{1}[0-9]{1}([0-2]{1}[0-9]{1}|3[0-1]{1})</validator>
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36 </param>
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37 <param name="amplicons" type="text" label='Select database to download by amplicons, put an amplicons list separated by "," ' help='example: "COI,ITS,16S" or "23S"'/>
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38 <param name="bases" type="text" label='Select database to download by base, put a bases list separated by "," ' help='example: "SILVA,PR2,MIDAS" or "BOLD"'/>
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39 <param name="filters" type="text" label='Select database to download by filters, put a filters list separated by "," ' help='example: "Pintail100,Fungi"'/>
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40 </when>
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41 </conditional>
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42 <param name="only_last_versions" type="boolean" checked="true" label="Download only the last version of each database"/>
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43 </when>
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44 <when value="HVL_db_data"/>
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45 </conditional>
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46 </inputs>
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47 <outputs>
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48 <data name="output" format="data_manager_json"/>
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49 </outputs>
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50 <help><![CDATA[
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51 TODO: Fill in help.
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52 ]]></help>
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53 </tool>