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annotate data_manager_conf.xml @ 15:b67c24d902aa draft

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author jjohnson
date Tue, 12 Dec 2017 12:00:24 -0500
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b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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1 <?xml version="1.0"?>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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2 <data_managers>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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3 <data_manager tool_file="datamanager_create_reference.xml" id="data_manager_defuse_reference" >
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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4 <data_table name="defuse_reference"> <!-- Defines a Data Table to be modified. -->
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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5 <output> <!-- Handle the output of the Data Manager Tool -->
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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6 <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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7 <column name="dbkey" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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8 <column name="name" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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9 <column name="path" output_ref="out_file" > <!-- The value of this column will be modified based upon data in "out_file". example value "phiX.fa" -->
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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10 <move type="directory"> <!-- Moving a file from the extra files path of "out_file" -->
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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11 <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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12 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/defuse</target> <!-- Target Location to store the file, directories are created as needed -->
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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13 </move>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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14 <!-- datamanager_create_reference.py should have copied the defuse config file to the working directory.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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15 so if we put the ${dbkey}.config path in this column, defuse.xml can set the data_directory to this this directory.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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16 -->
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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17 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${value}/defuse/${value}.config</value_translation> <!-- Store this value in the final Data Table -->
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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18 <value_translation type="function">abspath</value_translation>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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19 </column>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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20 </output>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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21 </data_table>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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22 </data_manager>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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23 </data_managers>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
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