Mercurial > repos > iuc > amrfinderplus_data_manager_build

annotate data_manager/data_manager_build_amrfinderplus.xml @ 3:dfa1eb2941b0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
author iuc
date Sun, 23 Nov 2025 12:21:34 +0000
parents a5921c09b7b7
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eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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1 <tool id="data_manager_build_amrfinderplus" name="amrfinderplus_datamanager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>AMRFinderPlus database builder</description>
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eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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3 <macros>
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iuc
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4 <import>macro.xml</import>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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5 </macros>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
2
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9 python '$__tool_directory__/data_manager_build_amrfinderplus.py'
a5921c09b7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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10 '$output_file'
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11 --db_version '$database_list.database_version_select'
a5921c09b7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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12 #if $database_list.database_version_select != 'latest':
a5921c09b7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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13 --db_date '$database_list.database_date_select'
a5921c09b7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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14 #end if
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15 $test_data_manager
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16 ]]></command>
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17 <inputs>
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18 <conditional name="database_list">
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19 <param name="database_version_select" type="select" label="Database version">
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20 <option value="4.0">V4.0</option>
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21 <option value="3.12">V3.12</option>
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22 </param>
3
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23 <when value="4.0">
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24 <param name="database_date_select" type="select" label="Date version">
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25 <option value="2025-07-16.1">2025-07-16.1</option>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
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26 </param>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
iuc
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27 </when>
2
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28 <when value="3.12">
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eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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29 <param name="database_date_select" type="select" label="Date version">
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30 <option value="2024-05-02.2">2024-05-02.2</option>
a5921c09b7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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31 <option value="2024-01-31.1">2024-01-31.1</option>
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32 </param>
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33 </when>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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34 </conditional>
3
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35 <param name="test_data_manager" type="hidden" value=""/>
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eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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36 </inputs>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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37 <outputs>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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38 <data name="output_file" format="data_manager_json"/>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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39 </outputs>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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40 <tests>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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41 <!-- Test_1 DB latest -->
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42 <test expect_num_outputs="1">
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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43 <param name="test_data_manager" value="--test"/>
1
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44 <output name="output_file">
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45 <assert_contents>
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46 <has_n_lines n="1"/>
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47 <has_text text="{&quot;data_tables&quot;"/>
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48 <has_text text="amrfinderplus_versioned_database"/>
1
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49 </assert_contents>
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50 </output>
0
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51 </test>
2
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52 <!-- Test_2 DB 3.12 2024-01-31.1 -->
0
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53 <test expect_num_outputs="1">
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54 <param name="test_data_manager" value="--test"/>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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55 <conditional name="database_list">
2
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56 <param name="database_version_select" value="3.12"/>
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57 <param name="database_date_select" value="2024-01-31.1"/>
0
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58 </conditional>
2
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59 <output name="output_file">
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60 <assert_contents>
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61 <has_n_lines n="1"/>
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62 <has_text text="{&quot;data_tables&quot;"/>
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63 <has_text text="amrfinderplus_versioned_database"/>
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64 <has_text text='"name": "V3.12-2024-01-31.1"'/>
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65 <has_text text='"db_version": "3.12"'/>
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66 </assert_contents>
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67 </output>
0
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68 </test>
3
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69 <!-- Test_3 DB 4.0 2025-07-16.1 -->
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70 <test expect_num_outputs="1">
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71 <param name="test_data_manager" value="--test"/>
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72 <conditional name="database_list">
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73 <param name="database_version_select" value="4.0"/>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
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74 <param name="database_date_select" value="2025-07-16.1"/>
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75 </conditional>
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76 <output name="output_file">
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77 <assert_contents>
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78 <has_n_lines n="1"/>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
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79 <has_text text="{&quot;data_tables&quot;"/>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
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80 <has_text text="amrfinderplus_versioned_database"/>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
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81 <has_text text='"name": "V4.0-2025-07-16.1"'/>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
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82 <has_text text='"db_version": "4.0"'/>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
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83 </assert_contents>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
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84 </output>
dfa1eb2941b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_amrfinderplus commit 45dbbf06a59df43da2c321c272de11cc41e17d43
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85 </test>
0
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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86 </tests>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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87 <help><![CDATA[
2
a5921c09b7b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 991998a3bb25e0059a8441975c652c7a75063709
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88 Download AMRFinderPlus database from the NCBI server
0
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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89 ]]></help>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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90 <citations>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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91 <citation type="doi">10.1038/s41598-021-91456-0</citation>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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92 </citations>
eea0c38a9afd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_amrfinderplus commit 59077a173599fc9d355a5d36ad7875050dbe3e19
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93 </tool>