Mercurial > repos > ufz > iphop_build_database

annotate data_manager/iphop_datamanager.xml @ 3:39dc692a9554 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit 40d304560b0b732bcc2b6397a72964caf1a5a451
author ufz
date Wed, 18 Dec 2024 12:30:34 +0000
parents d636e6221f8e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
1 <tool id="iphop_build_database" name="iPHoP" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
2 <description>database builder</description>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
3 <macros>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
4 <token name="@TOOL_VERSION@">1.3.3</token>
3
39dc692a9554 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit 40d304560b0b732bcc2b6397a72964caf1a5a451
ufz
parents: 2
diff changeset
5 <token name="@VERSION_SUFFIX@">3</token>
0
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
6 <token name="@PROFILE@">22.01</token>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
7 </macros>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
8 <requirements>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
9 <requirement type="package" version="@TOOL_VERSION@">iphop</requirement>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
10 </requirements>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
11 <command detect_errors="exit_code"><![CDATA[
2
d636e6221f8e planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit c78bd5eafa3d9450305cc8b32ba9cf8c64c42ba7
ufz
parents: 1
diff changeset
12 mkdir -p '$out_file.extra_files_path'/db &&
0
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
13 iphop download
2
d636e6221f8e planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit c78bd5eafa3d9450305cc8b32ba9cf8c64c42ba7
ufz
parents: 1
diff changeset
14 --db_dir '$out_file.extra_files_path'/db
0
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
15 --db_version $db_version
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
16 ## --full_verify https://bitbucket.org/srouxjgi/iphop/issues/114/db-download-verification-error
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
17 --no_prompt &&
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
18 cp '$dmjson' '$out_file'
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
19 ]]></command>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
20 <configfiles>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
21 <configfile name="dmjson"><![CDATA[
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
22 {
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
23 "data_tables":{
1
26f850e35fa0 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit 129359f5f9b723bf69f75f43da58bf0d2e7d4378
ufz
parents: 0
diff changeset
24 "iphop":[
0
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
25 {
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
26 "path":"db",
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
27 "name":"Version $db_version",
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
28 "version":"$db_version",
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
29 "value":"$db_version"
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
30 }
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
31 ]
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
32 }
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
33 }]]>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
34 </configfile>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
35 </configfiles>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
36 <inputs>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
37 <param name="db_version" type="select" multiple="false" label="Database Version">
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
38 <option value="iPHoP_db_Aug23_rw">iPHoP_db_Aug23_rw</option>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
39 </param>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
40 </inputs>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
41 <outputs>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
42 <data name="out_file" format="data_manager_json" />
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
43 </outputs>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
44 <tests>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
45 <!-- <test expect_num_outputs="1">
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
46 <param name="db_version" value="iPHoP_db_Aug23_rw" />
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
47 <output name="out_file">
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
48 <assert_contents>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
49 <has_text text='"value":"iPHoP_db_Aug23_rw"'/>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
50 <has_text text='"name":"Version iPHoP_db_Aug23_rw"'/>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
51 </assert_contents>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
52 </output>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
53 </test> -->
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
54 </tests>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
55 <help><![CDATA[
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
56 Download and extract iPHoP reference data
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
57 ]]></help>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
58 <citations>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
59 <citation type="doi">10.1371/journal.pbio.3002083</citation>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
60 </citations>
5c31cd602239 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/data_managers/data_manager_iphop commit d99e4d279594b887549d2cea9b1f452c9b1b89c8
ufz
parents:
diff changeset
61 </tool>