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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 52575ece22fcdbb6fc3aa3582ea377075aaa4db1
author iuc
date Thu, 01 Sep 2022 17:14:59 +0000
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1 <tool id="dram_set_database_locations" name="DRAM: set database locations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>after installation by the data manager</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/dram_set_database_locations.py'
9 $skip_uniref
10 --db_version '$db_version'
11 --galaxy_data_manager_data_path '$galaxy_data_manager_data_path'
12 --output '$output'
13 ]]></command>
14 <inputs>
15 <param argument="--skip_uniref" type="boolean" truevalue="--skip_uniref" falsevalue="" checked="false" label="Did you skip downloading and processing uniref when you installed the DRAM databases?"/>
16 <param name="db_version" type="text" value="1.3.5" label="DRAM database version">
17 <expand macro="sanitizer"/>
18 </param>
19 <param name="galaxy_data_manager_data_path" type="text" value="" label="Absolute Galaxy data manager data path" help="This is the absolute path for the Galaxy tool-data config setting">
20 <expand macro="sanitizer"/>
21 </param>
22 </inputs>
23 <outputs>
24 <data name="output" format="txt"/>
25 </outputs>
26 <tests>
27 <test expect_failure="true">
28 <param name="skip_uniref" value="true"/>
29 <param name="galaxy_data_manager_data_path" value="/gx/tool-data"/>
30 <assert_stderr>
31 <has_text text="error: unrecognized arguments: db: None"/>
32 </assert_stderr>
33 </test>
34 </tests>
35 <help>
36 Use of this tool should be restricted to a Galaxy administrator. This tool updates the DRAM configuration file
37 with the location of the databases after installation by the data manager. This is necessary because DRAM creates
38 a configuration file during installation, but the file is written before the Galaxy job finishes, so the database
39 locations are relative to the job working directory instead of the configured GALAXY_DATA_MANAGER_DATA_PATH.
40
41 It may be more ideal to perform this task as a second step in the data manager tool, but DRAM will not allow
42 the configuration file to be updated to point to locations unless the databases exist in those locations. But
43 the data manager tool moves the databases to these locations as its last step, making it impossible to update
44 the DRAM configuration file as a second step of that tool.
45
46 See https://github.com/WrightonLabCSU/DRAM/wiki/5.-Managing%2C-updating-or-moving-a-DRAM-installation-and-databases for details.
47 </help>
48 <citations>
49 <citation type="doi">10.1093/nar/gkaa621</citation>
50 </citations>
51 </tool>
52