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annotate data_manager/FROGS_data_manager.xml @ 9:0d9cb5c5aa35 draft

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author dchristiany
date Mon, 07 Oct 2019 10:56:23 -0400
parents cac51639c40f
children 238a5328279d
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1 <tool id="FROGS_data_manager" name="FROGS Data manager" version="2019.10.07.1" 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 $database.database=="frogs_db_data"
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11 --custom_db="$database.db_type.custom_db"
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12 --amplicons="$database.db_type.amplicons"
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13 #end if
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14 --output "$output"
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15 ]]></command>
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16 <inputs>
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17 <conditional name="database">
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18 <param name="database" type="select" label="Please select a database to update">
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19 <option value="frogs_db_data">FROGS database (FROGS Affiliation OTU)</option>
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20 <option value="HVL_db_data">HVL database (FROGS Affiliation postprocess)</option>
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21 </param>
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22 <when value="frogs_db_data">
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23 <conditional name="db_type">
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24 <param name="custom_db" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Build a custom database"/>
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25 <when value="true">
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26 <param name="amplicons" type="select" multiple="true">
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27 <option value="COI_MIDORI_MARINE_20180221">COI MIDORI MARINE 20180221</option>
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28 <option value="COI_MIDORI_20180221">COI MIDORI 20180221</option>
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29 <option value="COI_BOLD_1percentN_600nt_022019">COI BOLD 1percentN 600nt 022019</option>
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30 <option value="COI_BOLD_1percentN_630nt_022019">COI BOLD 1percentN 630nt 022019</option>
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31 <option value="ITS_UNITE_Euka_8.0">ITS UNITE Euka 8.0</option>
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32 <option value="ITS_UNITE_Fungi_8.0">ITS UNITE Fungi 8.0</option>
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33 <option value="COI_BOLD_022019">COI BOLD 022019</option>
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34 <option value="COI_BOLD_1percentN_022019">COI BOLD 1percentN 022019</option>
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35 <option value="EF1,18S_PHYMYCO-DB_2013">EF1,18S PHYMYCO-DB 2013</option>
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36 <option value="16S_EZBioCloud_052018">16S EZBioCloud 052018</option>
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37 <option value="18S_PR2_4.11.0">18S PR2 4.11.0</option>
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38 <option value="16S_DAIRYdb_V1.1.2">16S DAIRYdb V1.1.2</option>
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39 <option value="rbcL_Rsyst_Diatom_7">rbcL Rsyst Diatom 7</option>
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40 <option value="ITS_UNITE_7.1">ITS UNITE 7.1</option>
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41 <option value="rpoB_DB_NAME_TO_CHECK_122017">rpoB DB NAME TO CHECK 122017</option>
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42 <option value="16S_SILVA_Pintail100_132">16S SILVA Pintail100 132</option>
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43 <option value="16S_SILVA_Pintail50_132">16S SILVA Pintail50 132</option>
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44 <option value="16S_SILVA_Pintail80_132">16S SILVA Pintail80 132</option>
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45 <option value="16S_SILVA_132">16S SILVA 132</option>
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46 <option value="18S_SILVA_132">18S SILVA 132</option>
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47 <option value="23S_SILVA_132">23S SILVA 132</option>
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48 <option value="16S_SILVA_Pintail100_128">16S SILVA Pintail100 128</option>
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49 <option value="16S_SILVA_Pintail50_128">16S SILVA Pintail50 128</option>
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50 <option value="16S_SILVA_Pintail80_128">16S SILVA Pintail80 128</option>
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51 <option value="18S_PR2_Gb203_4.5">18S PR2 Gb203 4.5</option>
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52 <option value="16S_MIDAS_S123_2.1.3">16S MIDAS S123 2.1.3</option>
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53 <option value="16S_SILVA_128">16S SILVA 128</option>
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54 <option value="18S_SILVA_123">18S SILVA 123</option>
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55 <option value="18S_SILVA_128">18S SILVA 128</option>
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56 <option value="23S_SILVA_128">23S SILVA 128</option>
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57 <option value="16S_MIDAS_S119_1.20">16S MIDAS S119 1.20</option>
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58 <option value="16S_Greengenes_13.5">16S Greengenes 13.5</option>
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59 <option value="16S_SILVA_123">16S SILVA 123</option>
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60 <option value="18S_SILVA_119-1">18S SILVA 119-1</option>
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61 <option value="23S_SILVA_123">23S SILVA 123</option>
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62 </param>
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63 </when>
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64 </conditional>
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65 </when>
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66 <when value="HVL_db_data"/>
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67 </conditional>
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68 </inputs>
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69 <outputs>
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70 <data name="output" format="data_manager_json"/>
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71 </outputs>
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72 <help><![CDATA[
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73 TODO: Fill in help.
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74 ]]></help>
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75 </tool>