Mercurial > repos > iuc > data_manager_omamer
annotate data_manager/omamer.xml @ 2:f8d72275878e draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
author | iuc |
---|---|
date | Wed, 14 Aug 2024 15:42:46 +0000 |
parents | 57db282ca204 |
children |
rev | line source |
---|---|
1
57db282ca204
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd
iuc
parents:
0
diff
changeset
|
1 <tool id="data_manager_omamer" name="OMAmer data manager" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="20.01"> |
0
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
2 <macros> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
3 <import>macros.xml</import> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
4 </macros> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
5 <version_command></version_command> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
6 <command detect_errors="exit_code"><![CDATA[ |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
7 python '$__tool_directory__/omamer.py' |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
8 --name '$name' |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
9 --json '$output_file' |
1
57db282ca204
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd
iuc
parents:
0
diff
changeset
|
10 --version '@TOOL_VERSION@' |
0
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
11 ]]></command> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
12 <inputs> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
13 <param name="output_dir" type="text" label="Output Directory" value=""/> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
14 <param name="name" type="select" label="Database"> |
2
f8d72275878e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
iuc
parents:
1
diff
changeset
|
15 <option value="Primates_v2.0.0">Primates_v2.0.0</option> |
f8d72275878e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
iuc
parents:
1
diff
changeset
|
16 <option value="Viridiplantae_v2.0.0">Viridiplantae_v2.0.0</option> |
f8d72275878e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
iuc
parents:
1
diff
changeset
|
17 <option value="Metazoa_v2.0.0">Metazoa_v2.0.0</option> |
f8d72275878e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
iuc
parents:
1
diff
changeset
|
18 <option value="LUCA_v0.2.5">LUCA_v0.2.5</option> |
f8d72275878e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
iuc
parents:
1
diff
changeset
|
19 <option value="LUCA_v2.0.0">LUCA_v2.0.0</option> |
f8d72275878e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
iuc
parents:
1
diff
changeset
|
20 <option value="Saccharomyceta">Saccharomyceta</option> |
f8d72275878e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
iuc
parents:
1
diff
changeset
|
21 <option value="Homininae">Homininae</option> |
0
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
22 </param> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
23 </inputs> |
1
57db282ca204
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd
iuc
parents:
0
diff
changeset
|
24 |
0
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
25 <outputs> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
26 <data name="output_file" format="data_manager_json" label="OMAmer data manager: JSON"/> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
27 </outputs> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
28 |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
29 <tests> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
30 <test> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
31 <param name="output_dir" value="test_galaxy"/> |
2
f8d72275878e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit b890cd87ef5cfaa81eda29cc935de224ecb05bb6
iuc
parents:
1
diff
changeset
|
32 <param name="name" value="Primates_v2.0.0"/> |
1
57db282ca204
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd
iuc
parents:
0
diff
changeset
|
33 <output name="output_file" file="out.json"/> |
0
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
34 </test> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
35 </tests> |
1
57db282ca204
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd
iuc
parents:
0
diff
changeset
|
36 |
0
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
37 <help><![CDATA[ |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
38 This data manager retrieves data from various pre-built databases. |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
39 |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
40 .. _omamer: https://github.com/DessimozLab/omamer |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
41 ]]></help> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
42 <citations> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
43 <citation type="doi">10.1093/bioinformatics/btab219</citation> |
e1502e4f8725
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 8ff9ada22d22cb94ddfff51bcdd3ab7d30104f1a
iuc
parents:
diff
changeset
|
44 </citations> |
1
57db282ca204
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_omamer commit 67067cd7917545904b3a9980948abdd19f0576bd
iuc
parents:
0
diff
changeset
|
45 </tool> |