Mercurial > repos > iuc > data_manager_funannotate
annotate data_manager/funannotate.xml @ 1:1a0230433e1a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
| author | iuc |
|---|---|
| date | Thu, 18 Nov 2021 21:49:27 +0000 |
| parents | 22777795bb5f |
| children | 28fc15925666 |
| rev | line source |
|---|---|
|
1
1a0230433e1a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents:
0
diff
changeset
|
1 <tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.2" tool_type="manage_data" profile="20.01"> |
|
0
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
2 <requirements> |
|
1
1a0230433e1a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents:
0
diff
changeset
|
3 <requirement type="package" version="1.8.9">funannotate</requirement> |
|
1a0230433e1a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents:
0
diff
changeset
|
4 <requirement type="package" version="2.26.0">requests</requirement> |
|
0
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
5 </requirements> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
6 <version_command>funannotate check --show-versions</version_command> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
7 <command detect_errors="exit_code"><![CDATA[ |
|
1
1a0230433e1a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents:
0
diff
changeset
|
8 python -u '$__tool_directory__/funannotate.py' |
|
0
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
9 $partial_data |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
10 \$(date +'%Y-%m-%d-%H%M%S') |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
11 'funannotate' |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
12 '${output_file}' |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
13 ]]></command> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
14 <inputs> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
15 <param name="partial_data" type="hidden" value="" help="Used for testing"/> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
16 </inputs> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
17 <outputs> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
18 <data name="output_file" format="data_manager_json"/> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
19 </outputs> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
20 <tests> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
21 <test> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
22 <param name="partial_data" value="--partial"/> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
23 <output name="output_file"> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
24 <assert_contents> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
25 <has_text text="Funannotate database "/> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
26 <has_text text='"format_version": "1.0"'/> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
27 </assert_contents> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
28 </output> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
29 </test> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
30 </tests> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
31 <help><![CDATA[ |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
32 This data managers fetches data from various databases for the funannotate |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
33 annotation tool and updates the funannotate data table. |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
34 |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
35 .. _funannotate: https://funannotate.readthedocs.io |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
36 ]]></help> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
37 <citations> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
38 <citation type="doi">10.5281/zenodo.4054262</citation> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
39 </citations> |
|
22777795bb5f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff
changeset
|
40 </tool> |