Mercurial > repos > bgruening > data_manager_sylph_database

annotate data_manager/data_manager_sylph_database.xml @ 0:2ea34d422df4 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
author bgruening
date Fri, 23 May 2025 09:47:40 +0000
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2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
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1 <tool id="data_manager_sylph_database" name="Download pre-built sylph databases" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="@PROFILE@">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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2 <description></description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.8.1</token>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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5 <token name="@VERSION_SUFFIX@">0</token>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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6 <token name="@PROFILE@">23.0</token>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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7 <token name="@DB_VERSION@">1</token>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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8 </macros>
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9 <requirements>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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10 <requirement type="package" version="@TOOL_VERSION@">sylph</requirement>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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13
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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14 #set $file = str($db_link).split('/')[-1]
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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15
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16 mkdir -p '$out_file.extra_files_path' &&
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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17 wget $db_link &&
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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18 mv '$file' '$out_file.extra_files_path' &&
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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19 cp '$dmjson' '$out_file'
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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20 ]]></command>
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21 <configfiles>
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22 <configfile name="dmjson"><![CDATA[
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23 #from datetime import date
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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24 #set $file = str($db_link).split('/')[-1]
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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25
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26 {
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27 "data_tables":{
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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28 "sylph_databases":[
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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29 {
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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30 "value": "sylph_downloaded_#echo date.today().strftime('%d%m%Y')#_${file}",
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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31 "name": "sylph database ${file}",
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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32 "path": "${file}",
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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33 "clade": "${clades}",
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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34 "sylph_tax_identifier": "${name}",
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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35 "version": "@DB_VERSION@"
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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36 }
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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37 ]
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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38 }
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39 }]]></configfile>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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40 </configfiles>
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41 <inputs>
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42 <conditional name="db_type">
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43 <param argument="clades" type="select" label="Type of Databases">
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44 <option value="prokaryote">Prokaryote databases</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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45 <option value="eukaryote">Eukaryote databases</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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46 <option value="virus">Virus databases</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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47 </param>
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48 <when value="prokaryote">
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49 <conditional name="db_name">
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50 <param argument="name" type="select" label="Database">
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51 <option value="GTDB_r220">GTDB r220</option>
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52 <option value="GTDB_r214">GTDB r214</option>
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53 <option value="OceanDNA">Ocean DNA</option>
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54 <option value="SoilSMAG">Soil MAGs</option>
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55 </param>
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56 <when value="GTDB_r220">
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57 <param name="db_link" type="select" label="Sylph prokaryote databases">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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58 <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r220-c200-dbv1.syldb" selected="true">GTDB-r220 (April 2024) -c 200, more sensitive database</option>
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59 <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/gtdb-r220-c1000-dbv1.syldb">GTDB-r220 (April 2024) -c 1000 more efficient, less sensitive database</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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60 </param>
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61 </when>
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62 <when value="GTDB_r214">
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63 <param name="db_link" type="select" label="Sylph prokaryote databases">
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64 <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/v0.3-c200-gtdb-r214.syldb">GTDB-r214 (April 2023) -c 200, more sensitive database</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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65 <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/v0.3-c1000-gtdb-r214.syldb">GTDB-r214 (April 2023) -c 1000 more efficient, less sensitive database</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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66 </param>
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67 </when>
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68 <when value="OceanDNA">
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69 <param name="db_link" type="select" label="Sylph prokaryote databases">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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70 <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/OceanDNA-c200-v0.3.syldb">OceanDNA - ocean MAGs from Nishimura and Yoshizawa, -c 200, more sensitive database</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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71 </param>
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72 </when>
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73 <when value="SoilSMAG">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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74 <param name="db_link" type="select" label="Sylph prokaryote databases">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
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75 <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/SMAG-c200-v0.3.syldb">SoilSMAG (SMAG) from Ma et al. -c 200, more sensitive database</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
76 </param>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
77 </when>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
78 </conditional>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
79 </when>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
80 <when value="eukaryote">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
81 <conditional name="db_name">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
82 <param argument="name" type="select" label="Database">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
83 <option value="FungiRefSeq-2024-07-25">Refseq fungi 2024-07-25</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
84 <option value="TaraEukaryoticSMAG">TARA eukaryotic SMAGs</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
85 </param>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
86 <when value="FungiRefSeq-2024-07-25">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
87 <param name="db_link" type="select" label="Sylph eukaryote databases">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
88 <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/fungi-refseq-2024-07-25-c200-v0.3.syldb" selected="true">FungiRefSeq-2024-07-25 - Refseq fungi representative genomes collected on 2024-07-25</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
89 </param>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
90 </when>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
91 <when value="TaraEukaryoticSMAG">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
92 <param name="db_link" type="select" label="Sylph eukaryote databases">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
93 <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/tara-eukmags-c200-v0.3.syldb">TaraEukaryoticSMAG - TARA eukaryotic SMAGs from Delmont et al. -c 200, more sensitive database</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
94 </param>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
95 </when>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
96 </conditional>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
97 </when>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
98 <when value="virus">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
99 <conditional name="db_name">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
100 <param argument="name" type="select" label="Database">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
101 <option value="IMGVR_4.1">IMG/VR 4.1</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
102 </param>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
103 <when value="IMGVR_4.1">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
104 <param name="db_link" type="select" label="Sylph virus databases">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
105 <option value="http://faust.compbio.cs.cmu.edu/sylph-stuff/imgvr_c200_v0.3.0.syldb" selected="true">IMGVR_4.1 high-confidence viral OTU genomes, -c 200, more sensitive database</option>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
106 </param>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
107 </when>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
108 </conditional>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
109 </when>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
110 </conditional>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
111 </inputs>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
112 <outputs>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
113 <data name="out_file" format="data_manager_json" label="${tool.name}"/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
114 </outputs>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
115 <tests>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
116 <test expect_num_outputs="1">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
117 <conditional name="db_type">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
118 <param name="clades" value="eukaryote"/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
119 <conditional name="db_name">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
120 <param name="name" value="FungiRefSeq-2024-07-25"/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
121 <param name="db_link" value="http://faust.compbio.cs.cmu.edu/sylph-stuff/fungi-refseq-2024-07-25-c200-v0.3.syldb"/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
122 </conditional>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
123 </conditional>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
124 <output name="out_file">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
125 <assert_contents>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
126 <has_text text='"sylph_databases":'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
127 <has_text_matching expression='"value": "sylph_downloaded_[0-9]{8}_fungi-refseq-2024-07-25-c200-v0.3.syldb"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
128 <has_text text='"name": "sylph database fungi-refseq-2024-07-25-c200-v0.3.syldb"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
129 <has_text_matching expression='"path": "fungi-refseq-2024-07-25-c200-v0.3.syldb"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
130 <has_text text='"clade": "eukaryote"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
131 <has_text text='"sylph_tax_identifier": "FungiRefSeq-2024-07-25"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
132 <has_text text='"version": "@DB_VERSION@"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
133 </assert_contents>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
134 </output>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
135 </test>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
136 <test expect_num_outputs="1">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
137 <conditional name="db_type">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
138 <param name="clades" value="prokaryote"/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
139 <conditional name="db_name">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
140 <param name="name" value="OceanDNA"/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
141 <param name="db_link" value="http://faust.compbio.cs.cmu.edu/sylph-stuff/OceanDNA-c200-v0.3.syldb"/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
142 </conditional>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
143 </conditional>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
144 <output name="out_file">
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
145 <assert_contents>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
146 <has_text text='"sylph_databases":'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
147 <has_text_matching expression='"value": "sylph_downloaded_[0-9]{8}_OceanDNA-c200-v0.3.syldb"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
148 <has_text text='"name": "sylph database OceanDNA-c200-v0.3.syldb"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
149 <has_text_matching expression='"path": "OceanDNA-c200-v0.3.syldb"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
diff changeset
150 <has_text text='"clade": "prokaryote"'/>
2ea34d422df4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_sylph_database commit 6ac2834ca0a21512c9986e2fb8d0dcda1c4b0e18
bgruening
parents:
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151 <has_text text='"sylph_tax_identifier": "OceanDNA"'/>
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152 <has_text text='"version": "@DB_VERSION@"'/>
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153 </assert_contents>
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154 </output>
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155 </test>
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156 </tests>
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157 <help><![CDATA[
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158 This tool downloads pre-built sylph databases.
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159 -c: the compression parameter. Memory/runtime scale like 1/c; higher c is faster but less sensitive at low coverage.
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160 Default c = 200. The -c for genomes must be than sup or = the -c for reads (strict sup is allowed)
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161 ]]></help>
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162 <citations>
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163 <citation type="doi">10.1038/s41587-024-02412-y</citation>
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164 </citations>
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165 </tool>