Mercurial > repos > iuc > data_manager_manual

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:36:28 +0000
parents 0bed5ee5b74a
children
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ac682ae1c557 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
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1 <tool id="data_manager_manual" name="Manual Data Manager" version="0.0.3" tool_type="manage_data" profile="19.01">
0
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2 <options sanitize="False" />
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3 <description>Entry Builder</description>
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4 <command detect_errors="exit_code"><![CDATA[
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5 python '$__tool_directory__/data_manager_manual.py'
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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6 '${out_file}'
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7 --galaxy_data_manager_data_path '${__app__.config.galaxy_data_manager_data_path}'
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8 ]]></command>
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9 <inputs>
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10 <repeat name="data_tables" title="Data Table to define" min="1">
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11 <param name="data_table_name" type="select" multiple="False" optional="False" label="Choose Desired Data Table"
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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12 dynamic_options="galaxy_code_get_available_data_tables( __trans__ )" refresh_on_change="True"/>
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13 <repeat name="columns" title="Table Columns" min="1">
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14 <param name="data_table_column_name" type="select" multiple="False" optional="False" label="Column Name"
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15 dynamic_options="galaxy_code_get_available_data_table_columns( __trans__, data_table_name )" />
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16 <!-- <param name="data_table_column_name" type="text" label="Column Name"/> -->
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17 <param name="data_table_column_value" type="text" label="Value to use for data table column"/>
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18 <conditional name="is_path">
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19 <param name="is_path_selector" type="select" label="Value is a path">
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20 <option value="yes">Yes</option>
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21 <option value="no" selected="True">No</option>
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22 </param>
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23 <when value="yes">
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24 <param name="abspath" type="boolean" label="Apply abspath" checked="True" truevalue="abspath" falsevalue="" />
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25 </when>
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26 <when value="no"/>
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27 </conditional>
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28 </repeat>
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29 </repeat>
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30 <repeat name="directory_content" title="Directory Content">
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31 <param name="subdir" type="text" label="Place in Subdirectory" value=""/>
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32 <conditional name="file_source">
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33 <param name="file_source_selector" type="select" label="File Content Source">
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34 <option value="history">History Item</option>
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35 <option value="URL" selected="True">URL</option>
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36 </param>
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37 <when value="history">
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38 <param name="file_history" type="data" multiple="false" optional="false" format="data" label="File from history" />
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39 </when>
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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40 <when value="URL">
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41 <param name="file_URL" type="text" label="Fetch from URL" value=""/>
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42 </when>
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43 </conditional>
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44 <conditional name="file_action">
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45 <param name="file_action_selector" type="select" label="File Actions">
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46 <option value="unpack">Extract Archive</option>
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47 <option value="None" selected="True">None</option>
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48 </param>
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49 <when value="None">
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50 <param name="filename_override" type="text" label="Override with Filename" value=""/>
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51 </when>
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52 <when value="unpack">
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53 </when>
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54 </conditional>
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55 </repeat>
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56 </inputs>
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57 <outputs>
10
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58 <data name="out_file" format="data_manager_json"/>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <repeat name="data_tables">
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63 <param name="data_table_name" value="__dbkeys__"/>
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64 <repeat name="columns">
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65 <param name="data_table_column_name" value="value"/>
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66 <param name="data_table_column_value" value="dm6"/>
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67 </repeat>
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68 <repeat name="columns">
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69 <param name="data_table_column_name" value="name"/>
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70 <param name="data_table_column_value" value="Drosophila melanogaster genome release 6"/>
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71 </repeat>
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72 <repeat name="columns">
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73 <param name="data_table_column_name" value="len_path"/>
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74 <param name="data_table_column_value" value="dm6.len"/>
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75 </repeat>
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76 </repeat>
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77 <output name="out_file" file="dm6.data_manager_json"/>
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78 </test>
0
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79 </tests>
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80 <help>
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81 **What it does**
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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82
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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83 This tool allows manually specifying data table entries and optionally providing filesystem contents.
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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84
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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85 </help>
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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86 <code file="data_manager_manual.py" />
81ed42c0721a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_manual commit 9f2cdfc1302dce000f9a86d13d4af204cf1dc89d
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87 </tool>