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annotate data_manager/data_manager_rsync.xml @ 0:70afa70bba41 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
author devteam
date Fri, 06 Nov 2015 14:18:13 -0500
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70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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1 <tool id="data_manager_rsync_g2" name="Rsync with g2" version="0.0.1" tool_type="manage_data">
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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2 <options sanitize="False" />
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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3 <description>fetching</description>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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4 <command interpreter="python">data_manager_rsync.py "${out_file}"</command>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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5 <stdio>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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6 <exit_code range="1:" err_level="fatal" />
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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7 <exit_code range=":-1" err_level="fatal" />
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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8 </stdio>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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9 <inputs>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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11 <param name="dbkey" type="genomebuild" label="dbkey to search for Reference Data" help="Specify ? to show all"/>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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13 <param name="data_table_names" type="select" display="checkboxes" multiple="True" optional="True"
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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14 label="Choose Desired Data Tables" dynamic_options="galaxy_code_get_available_data_tables( __trans__ )"
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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15 refresh_on_change="dbkey"/>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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18 <param name="data_table_entries" type="select" display="checkboxes" multiple="True" optional="False"
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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19 label="Choose Desired Data Tables Entries" dynamic_options="galaxy_code_get_available_data_tables_entries( __trans__, dbkey, data_table_names )"
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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20 refresh_on_change="dbkey"/>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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21 </inputs>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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22 <outputs>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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23 <data name="out_file" format="data_manager_json" dbkey="dbkey"/>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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24 </outputs>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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25 <tests>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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26 <test>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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27 <param name="dbkey" value="sacCer2"/>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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28 <param name="data_table_names" value="all_fasta"/>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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29 <param name="data_table_entries" value="eyJlbnRyeSI6IHsicGF0aCI6ICIvZ2FsYXh5L2RhdGEvc2FjQ2VyMi9zZXEvc2FjQ2VyMi5mYSIs ICJkYmtleSI6ICJzYWNDZXIyIiwgInZhbHVlIjogInNhY0NlcjIiLCAibmFtZSI6ICJZZWFzdCAo U2FjY2hhcm9teWNlcyBjZXJldmlzaWFlKTogc2FjQ2VyMiJ9LCAibmFtZSI6ICJhbGxfZmFzdGEi fQ=="/>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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30 <output name="out_file" file="sacCer2_rsync_all_fasta.data_manager_json"/>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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31 </test>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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32 </tests>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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33 <help>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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34 **What it does**
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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36 This tool connects to the Galaxy Project's rsync reference data repository to download data and populate tool data tables.
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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38 ------
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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42 .. class:: infomark
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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44 **Notice:** If you do not have a particular data table defined, then it will be created and persisted dynamically.
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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45
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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46 </help>
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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47 <code file="data_manager_rsync.py" />
70afa70bba41 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 86cf90107482cab1cb47fc0d42d6705f8077daa7
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48 </tool>