Mercurial > repos > iuc > data_manager_ncbi_taxonomy_sqlite
annotate data_manager/data_manager_ncbi_taxonomy_sqlite.xml @ 0:7a76cd412252 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
author | iuc |
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date | Tue, 21 Jul 2020 17:04:41 -0400 |
parents | |
children | 54a0869d0051 |
rev | line source |
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0
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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1 <tool id="data_manager_ncbi_taxonomy_sqlite" name="NCBI Taxonomy SQLite builder" tool_type="manage_data" profile="18.09" version="@PACKAGE_VERSION@+galaxy1" python_template_version="3.5"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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2 <macros> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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3 <token name="@PACKAGE_VERSION@">1.0.5</token> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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4 </macros> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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5 <requirements> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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6 <requirement type="package" version="@PACKAGE_VERSION@">rust-ncbitaxonomy</requirement> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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7 <requirement type="package" version="3.7">python</requirement> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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8 </requirements> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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9 <command detect_errors="exit_code"><![CDATA[ |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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10 #if $taxonomy.taxonomy_source == 'cached': |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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11 #set $taxonomy_dir = $taxonomy.taxonomy_table.fields.path |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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12 #else |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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13 mkdir taxonomy && ln -s '$taxonomy.nodes' taxonomy/nodes.dmp && ln -s '$taxonomy.names' taxonomy/names.dmp && |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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14 #set $taxonomy_dir = 'taxonomy' |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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15 #end if |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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16 python '$__tool_directory__/data_manager_ncbi_taxonomy_sqlite.py' '$taxonomy_dir' '$name' '$description' '$output_file' |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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17 ]]></command> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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18 <inputs> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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19 <conditional name="taxonomy"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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20 <param name="taxonomy_source" type="select" label="Choose source of NCBI Taxonomy"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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21 <option value="cached" selected="true">Use built-in NCBI Taxonomy database</option> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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22 <option value="history">Datasets from history</option> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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23 </param> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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24 <when value="cached"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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25 <param type="select" name="taxonomy_table" label="NCBI Taxonomy database"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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26 <options from_data_table="ncbi_taxonomy"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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27 <filter type="sort_by" column="1" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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28 <validator type="no_options" message="No NCBI Taxonomy downloads are available" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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29 </options> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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30 <validator type="no_options" message="No NCBI Taxonomy database download is available" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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31 </param> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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32 </when> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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33 <when value="history"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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34 <param name="nodes" type="data" format="txt" label="NCBI Taxonomy nodes.dmp file" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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35 <param name="names" type="data" format="txt" label="NCBI Taxonomy names.dmp file" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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36 </when> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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37 </conditional> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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38 <param name="name" type="text" label="Name of taxonomy database" help="(leave blank to use name based on today's date)" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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39 <param name="description" type="text" label="Description of taxonomy database" help="(leave blank to use name based on today's date)" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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40 </inputs> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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41 <outputs> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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42 <data name="output_file" format="data_manager_json"/> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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43 </outputs> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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44 <tests> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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45 <test> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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46 <conditional name="taxonomy"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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47 <param name="taxonomy_source" value="history" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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48 <param name="nodes" ftype="txt" value="taxdb/nodes.dmp" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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49 <param name="names" ftype="txt" value="taxdb/names.dmp" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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50 </conditional> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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51 <param name="name" value="test" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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52 <param name="description" value="test database" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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53 <output name="output_file"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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54 <assert_contents> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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55 <has_text text="tax.ncbitaxonomy.sqlite" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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56 <has_text text="test database" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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57 </assert_contents> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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58 </output> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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59 </test> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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60 <test> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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61 <conditional name="taxonomy"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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62 <param name="taxonomy_source" value="cached" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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63 <param name="taxonomy_table" value="sample" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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64 </conditional> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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65 <param name="name" value="test" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
parents:
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66 <param name="description" value="test database" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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67 <output name="output_file"> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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68 <assert_contents> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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69 <has_text text="tax.ncbitaxonomy.sqlite" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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70 <has_text text="test database" /> |
7a76cd412252
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_ncbi_taxonomy_sqlite/ commit bad9f3d1468b454b1ac073fa796e66b1d0164d38"
iuc
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71 </assert_contents> |
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72 </output> |
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73 </test> |
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74 </tests> |
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75 <help><![CDATA[ |
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76 The data manager creates a SQLite version the NCBI Taxonomy database, using the plain text files of the |
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77 NCBI database as input. Storing the database as a SQLite database allows for faster querying. |
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78 |
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79 Input is either from the individual files (nodes.dmp and names.dmp) from the NCBI Taxonomy database or |
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80 from a previously downloaded code of the database stored as "reference data" in the Galaxy server. |
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81 |
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82 .. class: infomark |
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83 |
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84 *Notice:** If you leave name, or description blank, it will be generated automatically from the current date. |
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85 ]]></help> |
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86 <citations> |
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87 <citation type="bibtex">@misc{vanHeusen2020, |
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88 author = {van Heusden, P.}, |
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89 title = {a Rust crate for working with a local copy of the NCBI Taxonomy database }, |
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90 year = {2020}, |
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91 publisher = {GitHub}, |
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92 journal = {GitHub repository}, |
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93 howpublished = {\url{https://github.com/pvanheus/ncbitaxonomy}}, |
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94 commit = {84d79cdcf2adb262c61511f8c7b9eceb5299b87d} |
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95 } |
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96 </citation> |
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97 </citations> |
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98 </tool> |