Mercurial > repos > iuc > data_manager_metaphlan_database_downloader
annotate data_manager/data_manager_metaphlan_download.xml @ 3:4ba60cb14cb0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
author | iuc |
---|---|
date | Wed, 05 Apr 2023 15:01:49 +0000 |
parents | 5fe20c915fa6 |
children | 0cb27ea69dc1 |
rev | line source |
---|---|
2
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
1 <tool id="data_manager_metaphlan_download" name="Download and build MetaPhlAn database" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05"> |
0
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
2 <description></description> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
3 <requirements> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
4 <requirement type="package" version="@TOOL_VERSION@">metaphlan</requirement> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
5 </requirements> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
6 <macros> |
2
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
7 <token name="@TOOL_VERSION@">4.0.6</token> |
3
4ba60cb14cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
parents:
2
diff
changeset
|
8 <token name="@VERSION_SUFFIX@">1</token> |
0
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
9 </macros> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
10 <stdio> |
2
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
11 <exit_code range=":-1" level="fatal" description="Error: Cannot open file"/> |
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
12 <exit_code range="1:" level="fatal" description="Error"/> |
0
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
13 </stdio> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
14 <command><![CDATA[ |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
15 python '$__tool_directory__/data_manager_metaphlan_download.py' |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
16 --index '$index' |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
17 --json '$out_file' |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
18 ]]></command> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
19 <inputs> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
20 <param name="index" type="select" label="Version"> |
3
4ba60cb14cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
parents:
2
diff
changeset
|
21 <option value="mpa_vOct22_CHOCOPhlAnSGB_202212" selected="true">FULL: mpa_vOct22_CHOCOPhlAnSGB_202212</option> |
4ba60cb14cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
parents:
2
diff
changeset
|
22 <option value="mpa_vJan21_CHOCOPhlAnSGB_202103">FULL: mpa_vJan21_CHOCOPhlAnSGB_202103</option> |
4ba60cb14cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
parents:
2
diff
changeset
|
23 <option value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103">DEMO: mpa_vJan21_TOY_CHOCOPhlAnSGB_202103</option> |
0
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
24 </param> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
25 </inputs> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
26 <outputs> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
27 <data name="out_file" format="data_manager_json" label="${tool.name}"/> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
28 </outputs> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
29 <tests> |
2
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
30 <test expect_num_outputs="1"> |
3
4ba60cb14cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
parents:
2
diff
changeset
|
31 <param name="index" value="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/> |
2
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
32 <output name="out_file"> |
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
33 <assert_contents> |
3
4ba60cb14cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
parents:
2
diff
changeset
|
34 <has_text text="mpa_vJan21_TOY_CHOCOPhlAnSGB_202103"/> |
4ba60cb14cb0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit f5c02de49bb33445667dd359bc7ce5801140b207
iuc
parents:
2
diff
changeset
|
35 <has_text text="MetaPhlAn clade-specific marker genes (mpa_vJan21_TOY_CHOCOPhlAnSGB_202103)"/> |
2
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
36 </assert_contents> |
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
37 </output> |
5fe20c915fa6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 57df6e8a0ffd145e560f7c7e20cfedbbe2ce01d2
iuc
parents:
1
diff
changeset
|
38 </test> |
0
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
39 </tests> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
40 <help><![CDATA[ |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
41 This tool downloads and builds the MetaPhlAn databases. |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
42 ]]></help> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
43 <citations> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
44 <citation type="doi">1101/2020.11.19.388223</citation> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
45 <yield /> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
46 </citations> |
169b08c9713c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_metaphlan_database_downloader commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
iuc
parents:
diff
changeset
|
47 </tool> |