Mercurial > repos > ieguinoa > data_manager_salmon_index_builder

comparison data_manager_conf.xml @ 1:c5dea2080109 draft

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author ieguinoa
date Tue, 14 Aug 2018 11:19:49 -0400
parents 6cd60ba8a842
children 3888ec1918d0
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0:6cd60ba8a842 1:c5dea2080109
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <data_managers> 2 <data_managers>
3 <data_manager tool_file="data_manager/data_manager_fetch_gff.xml" id="data_manager_fetch_gff"> 3 <data_manager tool_file="data_manager/salmon_index_builder.xml" id="salmon_index_builder" version="0.1">
4 <data_table name="all_gff"> 4 <data_table name="salmon_indexes">
5 <output> 5 <output>
6 <column name="value" /> 6 <column name="value" />
7 <column name="dbkey" /> 7 <column name="dbkey" />
8 <column name="name" /> 8 <column name="name" />
9 <column name="path" output_ref="out_file"> 9 <column name="path" output_ref="out_file" >
10 <move type="file"> 10 <move type="directory" relativize_symlinks="True">
11 <source>${path}</source> 11 <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
12 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/gff/${path}</target> 12 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/salmon_index/${value}</target>
13 </move> 13 </move>
14 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/gff/${path}</value_translation> 14 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/salmon_index/${value}/${path}</value_translation>
15 <value_translation type="function">abspath</value_translation>
16 </column>
17 </output>
18 </data_table>
19 <data_table name="representative_gff">
20 <output>
21 <column name="value" />
22 <column name="dbkey" />
23 <column name="name" />
24 <column name="path" output_ref="out_file">
25 <move type="file">
26 <source>${path}</source>
27 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/representative_gff/${path}</target>
28 </move>
29 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/representative_gff/${path}</value_translation>
30 <value_translation type="function">abspath</value_translation> 15 <value_translation type="function">abspath</value_translation>
31 </column> 16 </column>
32 </output> 17 </output>
33 </data_table> 18 </data_table>
34 </data_manager> 19 </data_manager>