Mercurial > repos > ecology > retrieve_bold

annotate retrieve_bold.xml @ 0:485e1d2753a2 draft default tip

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planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
author ecology
date Fri, 21 Jun 2024 08:55:36 +0000
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0
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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diff changeset
1 <tool id="retrieve_bold" name="Retrieve bold" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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2 <description>Functions to search in Bold and download the available sequences of each subtaxa (get_fasta)</description>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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3 <macros>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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4 <token name="@TOOL_VERSION@">1.3.0</token>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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5 <token name="@VERSION_SUFFIX@">0</token>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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6 </macros>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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7 <requirements>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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8 <requirement type="package" version="4.3.3">r-base</requirement>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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9 <requirement type="package" version="@TOOL_VERSION@">r-bold</requirement>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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10 </requirements>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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11 <command detect_errors="exit_code"><![CDATA[
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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12
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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13 Rscript
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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14 '$__tool_directory__/retrieve_bold.R' 1>Log.txt
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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15 ${taxa_list}
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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16 ${animal_marker.marker}
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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17 ${vegetal_marker.marker}
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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18 ${bacterial_marker.marker}
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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19 ${fungal_marker.marker}
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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20 ${protist_marker.marker}
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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21
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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22 ]]></command>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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23 <inputs>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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24 <param name ="taxa_list" type="data" format="txt"
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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25 label="" help="Provide a taxa list from which sequences will be extracted in the BOLD database"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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26 <section name="animal_marker" title= "Animal marker" expanded="false">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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27 <param name ="marker" type="select" checked="true" multiple="true"
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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28 label="" help="Provide a marker to search in the BOLD database">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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29 <option value="12S">12S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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30 <option value="16S">16S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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31 <option value="18S">18S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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32 <option value="28S">28S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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33 <option value="COI-3P">CO1-3P</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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34 <option value="COI-5P">CO1-5P</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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35 <option value="COII">COII</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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36 <option value="COXIII">COXIII</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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37 <option value="CYTB">Cytb</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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38 <option value="H3">H3</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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39 <option value="ND1">ND1</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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40 <option value="ND2">ND2</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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41 <option value="ND3">ND3</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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42 <option value="ND4">ND4</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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43 <option value="ND4L">ND4L</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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44 <option value="ND5-0">ND5-0</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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45 <option value="ND6">ND6</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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46 </param>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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47 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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48 <section name="vegetal_marker" title= "Vegetal marker" expanded="false">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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49 <param name ="marker" type="select" checked="true" multiple="true"
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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50 label="" help="Provide a marker to search in the BOLD database">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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51 <option value="atpF-atpH">atpF-atpH</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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52 <option value="ITS">ITS</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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53 <option value="ITS2">ITS2</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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54 <option value="matK">matK</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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55 <option value="matK-like">matK like</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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56 <option value="trnH-psbA">trnH-psbA</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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57 <option value="trnL">trnL</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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58 <option value="trnL-F">trnL-F</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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59 <option value="psbK-psbI">psbK-psbI</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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60 <option value="rbcL">rbcL</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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61 <option value="rbcLa">rbcLa</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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62 <option value="rpoC1">rpoC1</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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63 <option value="rpoB">rpoB</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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64
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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65 </param>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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66 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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67 <section name="bacterial_marker" title= "Bacterial marker" expanded="false">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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68 <param name ="marker" type="select" checked="true" multiple="true"
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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69 label="" help="Provide a marker to search in the BOLD database">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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70 <option value="16S">16S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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71 <option value="COI-3P">CO1-3P</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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72 <option value="COI-5P">CO1-5P</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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73 <option value="CPN60">cpnN60</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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74 <option value="GND">Gnd</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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75 <option value="RPOB">rpoB</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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76 <option value="RIF">RIF</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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77 <option value="TUF">Tuf</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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78 </param>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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79 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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80 <section name="fungal_marker" title= "Fungal marker" expanded="false">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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81 <param name ="marker" type="select" checked="true" multiple="true"
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
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82 label="" help="Provide a marker to search in the BOLD database">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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83 <option value="5-8S">5-8S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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84 <option value="18S">18S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
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diff changeset
85 <option value="18S-V4">18S-V4</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
86 <option value="28S">28S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
87 <option value="atp6">atp6</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
88 <option value="Beta-tubulin">Beta tubulin</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
89 <option value="COI-3P">CO1-3P</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
90 <option value="COI-5P">CO1-5P</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
91 <option value="COII">COII</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
92 <option value="COXIII">COXIII</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
93 <option value="EF1-alpha">EF1-alpha</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
94 <option value="ITS">ITS</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
95 <option value="ITS1">ITS1</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
96 <option value="ITS2">ITS2</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
97 <option value="NBC-COI-5P">NBC-COI-5P</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
98 <option value="RPB1">RPB1</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
99 <option value="RPB2">RPB2</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
100 <option value="TEF1-alpha">TEF1 alpha</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
101 </param>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
102 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
103 <section name="protist_marker" title= "Protist marker" expanded="false">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
104 <param name ="marker" type="select" checked="true" multiple="true"
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
105 label="" help="Provide a marker to search in the BOLD database">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
106 <option value="18S">18S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
107 <option value="23S">23S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
108 <option value="28S">28S</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
109 <option value="COI-3P">CO1-3P</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
110 <option value="COI-5P">CO1-5P</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
111 <option value="ITS">ITS</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
112 <option value="RBCL">rbcL</option>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
113 </param>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
114 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
115 </inputs>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
116 <outputs>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
117 <collection name="datasets_output" type="list"
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
118 label="Datasets list">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
119 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" format="fasta" />
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
120 </collection>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
121 <data name="Log" from_work_dir="Log.txt" format="txt" label="Log message"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
122 </outputs>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
123 <tests>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
124 <test>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
125 <param name ="taxa_list" value="taxa.list" />
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
126 <section name="animal_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
127 <param name="marker" value="12S,16S,18S,28S,COI-3P,COI-5P,COII,COXIII,CYTB,H3,ND1,ND2,ND3,ND4,ND4L,ND5-0,ND6"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
128 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
129 <section name="vegetal_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
130 <param name="marker" value="atpF-atpH,ITS,ITS2,matK,matK-like,trnH-psbA,trnL,trnL-F,psbK-psbI,rbcL,rbcLa,rpoC1,rpoB"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
131 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
132 <section name="bacterial_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
133 <param name="marker" value="16S,COI-3P,COI-5P,CPN60,GND,RPOB,RIF,TUF"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
134 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
135 <section name="fungal_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
136 <param name="marker" value="5-8S,18S,18S-V4,28S,atp6,Beta-tubulin,COI-3P,COI-5P,COII,COXIII,EF1-alpha,ITS,ITS1,ITS2,NBC-COI-5P,RPB1,RPB2,TEF1-alpha"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
137 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
138 <section name="protist_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
139 <param name="marker" value="18S,23S,28S,COI-3P,COI-5P,ITS,RBCL"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
140 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
141 <output name="Log" file="Log_test1.txt" compare="diff"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
142 <output_collection name="datasets_output" type="list" count="3">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
143 <element name="Chitonidaebold" file="Chitonidaebold1.fasta" ftype="fasta"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
144 <element name="Ischnochitonidaebold" file="Ischnochitonidaebold.fasta" ftype="fasta"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
145 <element name="Leptochitonidaebold" file="Leptochitonidaebold.fasta" ftype="fasta"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
146 </output_collection>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
147 </test>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
148 <test>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
149 <param name ="taxa_list" value="taxa.list" />
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
150 <section name="animal_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
151 <param name="marker" value="None"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
152 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
153 <section name="vegetal_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
154 <param name="marker" value="None"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
155 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
156 <section name="bacterial_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
157 <param name="marker" value="None"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
158 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
159 <section name="fungal_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
160 <param name="marker" value="None"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
161 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
162 <section name="protist_marker">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
163 <param name="marker" value="None"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
164 </section>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
165 <output name="Log" file="Log_test2.txt" compare="diff"/>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
166 <output_collection name="datasets_output" type="list" count="0">
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
167 </output_collection>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
168 </test>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
169 <test>
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
parents:
diff changeset
170 <param name ="taxa_list" value="taxa.list" />
485e1d2753a2 planemo upload for repository https://github.com/wpearman1996/MARES_database_pipeline/tree/master commit 853190e24a7acfe02bbfb1c392ac55f9b9a9e7da
ecology
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171 <section name="animal_marker">
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172 <param name="marker" value="CYTB"/>
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173 </section>
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174 <section name="vegetal_marker">
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175 <param name="marker" value="None"/>
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176 </section>
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177 <section name="bacterial_marker">
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178 <param name="marker" value="None"/>
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179 </section>
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180 <section name="fungal_marker">
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181 <param name="marker" value="Beta-tubulin,RPB2"/>
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182 </section>
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183 <section name="protist_marker">
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184 <param name="marker" value="None"/>
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185 </section>
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186 <output name="Log" file="Log_test3.txt" compare="diff"/>
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187 <output_collection name="datasets_output" type="list" count="1">
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188 <element name="Chitonidaebold" file="Chitonidaebold2.fasta" ftype="fasta"/>
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189 </output_collection>
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190 </test>
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191 </tests>
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192 <help><![CDATA[
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193 .. class:: infomark
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194
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195 **What it does**
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196
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197 This tool helps you get one or multiple list of fasta sequences from BOLD corresponding to the taxa and markers you have specified :
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198 BOLD Systems <https://boldsystems.org/>
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199
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200 ____
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201
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202
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203 .. class:: infomark
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204
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205 **Input**
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206 A list of taxa in a txt format file and a selection of markers (one or more) from different organisms. The categories only exist to help users and diminish complexity. All markers selected will be researched for all provided taxa, therefore you don't need to specify the same marker in multiple categories.
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207
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208 ____
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209
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210
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211 .. class:: infomark
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212
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213
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214 **Output**
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215
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216 Each "Taxa" and "Markers" request will produce a fasta file, all files will be available in a collection. This tool will also produce a log message specifying the available markers for each taxa.
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217
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218 .. class:: warning
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219
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220 **If no marker are selected or the markers selected are not found for the taxa, the tool will not produce a file. If you need, you can check the markers available for the different taxa in the "Log message" produced**
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221
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222
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223 ]]></help>
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224 <citations>
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225 <citation type="doi">
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226 10.1038/s41597-020-0549-9
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227 </citation>
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228 </citations>
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229 </tool>