Mercurial > repos > iuc > data_manager_funannotate

annotate data_manager/funannotate.xml @ 3:0cadd0a04412 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/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 4e4b3194807681c1e436a5525bdc9597d2868b1f"
author iuc
date Fri, 19 Nov 2021 15:43:06 +0000
parents 13018941c6a0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
1 <tool id="data_manager_funannotate" name="Funannotate data manager" version="0.0.3" tool_type="manage_data" profile="20.01">
0
ef7f9e2f32f2 "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
8dff71edbce5 "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>
8dff71edbce5 "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
ef7f9e2f32f2 "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>
ef7f9e2f32f2 "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>
ef7f9e2f32f2 "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[
3
0cadd0a04412 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 4e4b3194807681c1e436a5525bdc9597d2868b1f"
iuc
parents: 2
diff changeset
8 #if $wget:
0cadd0a04412 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 4e4b3194807681c1e436a5525bdc9597d2868b1f"
iuc
parents: 2
diff changeset
9 ## Asked for wget, we assume there's a certificate problem on (at least) one
0cadd0a04412 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 4e4b3194807681c1e436a5525bdc9597d2868b1f"
iuc
parents: 2
diff changeset
10 ## of the many requested servers, force disable of all checks
0cadd0a04412 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 4e4b3194807681c1e436a5525bdc9597d2868b1f"
iuc
parents: 2
diff changeset
11 echo "check_certificate = off" > \$HOME/.wgetrc &&
0cadd0a04412 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 4e4b3194807681c1e436a5525bdc9597d2868b1f"
iuc
parents: 2
diff changeset
12 #end if
0cadd0a04412 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 4e4b3194807681c1e436a5525bdc9597d2868b1f"
iuc
parents: 2
diff changeset
13
1
8dff71edbce5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit d1ebc78155f57c87d8e82c9855b176428e9803ad"
iuc
parents: 0
diff changeset
14 python -u '$__tool_directory__/funannotate.py'
0
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
15 $partial_data
2
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
16 $wget
0
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
17 \$(date +'%Y-%m-%d-%H%M%S')
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
18 'funannotate'
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
19 '${output_file}'
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
20 ]]></command>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
21 <inputs>
ef7f9e2f32f2 "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" type="hidden" value="" help="Used for testing"/>
2
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
23 <param name="wget" type="boolean" truevalue="--wget" falsevalue="" checked="False" label="Download using wget" help="Try this if you get certificate errors"/>
0
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
24 </inputs>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
25 <outputs>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
26 <data name="output_file" format="data_manager_json"/>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
27 </outputs>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
28 <tests>
ef7f9e2f32f2 "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>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
30 <param name="partial_data" value="--partial"/>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
31 <output name="output_file">
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
32 <assert_contents>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
33 <has_text text="Funannotate database "/>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
34 <has_text text='"format_version": "1.0"'/>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
35 </assert_contents>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
36 </output>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
37 </test>
2
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
38 <test>
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
39 <param name="partial_data" value="--partial"/>
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
40 <param name="wget" value="True"/>
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
41 <output name="output_file">
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
42 <assert_contents>
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
43 <has_text text="Funannotate database "/>
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
44 <has_text text='"format_version": "1.0"'/>
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
45 </assert_contents>
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
46 </output>
13018941c6a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
iuc
parents: 1
diff changeset
47 </test>
0
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
48 </tests>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
49 <help><![CDATA[
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
50 This data managers fetches data from various databases for the funannotate
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
51 annotation tool and updates the funannotate data table.
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
52
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
53 .. _funannotate: https://funannotate.readthedocs.io
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
54 ]]></help>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
55 <citations>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
56 <citation type="doi">10.5281/zenodo.4054262</citation>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
57 </citations>
ef7f9e2f32f2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 9613152729099079c7465c3d5d42005ef22ca91e"
iuc
parents:
diff changeset
58 </tool>