Mercurial > repos > ufz > lm_get_projects
comparison get_projects.xml @ 0:713502c9a98f draft default tip
planemo upload for repository https://github.com/jw44lavo/galaxy-tools/blob/bgo/tools/lambdaminer/ commit 3f45cd07445498cefa73931cadf3d1115245ca1e
| author | ufz |
|---|---|
| date | Mon, 17 Mar 2025 20:35:10 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:713502c9a98f |
|---|---|
| 1 <tool id="lm_get_projects" name="Get LMDB Projects" version="0.1.0+galaxy0" profile="21.05"> | |
| 2 <requirements> | |
| 3 <requirement type="package" version="2.2.2">pandas</requirement> | |
| 4 <requirement type="package" version="2.9.9">psycopg2</requirement> | |
| 5 <requirement type="package" version="2.0.37">sqlalchemy</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 #if $test != "" | |
| 9 export LAMBDAMINER_CREDENTIALS="$__tool_directory__/test-data/$test"; | |
| 10 #end if | |
| 11 python '$__tool_directory__/get_projects.py' | |
| 12 --login-name '$__user_name__' | |
| 13 --output-file '$projects' | |
| 14 ]]></command> | |
| 15 <inputs> | |
| 16 <param name="test" type="hidden"/> | |
| 17 </inputs> | |
| 18 <outputs> | |
| 19 <data name="projects" format="csv"/> | |
| 20 </outputs> | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="test" value="test_credentials.json"/> | |
| 24 <output name="projects" value="test_projects.csv" compare="contains"/> | |
| 25 </test> | |
| 26 <test expect_failure="true"> | |
| 27 <param name="test" value="test_credentials_false.json"/> | |
| 28 </test> | |
| 29 <test expect_failure="true"> | |
| 30 <param name="test" value="test_credentials_nonexistent.json"/> | |
| 31 </test> | |
| 32 </tests> | |
| 33 <help><![CDATA[ | |
| 34 **What it does** | |
| 35 | |
| 36 This tool queries the Lambda-Miner database for the users projects. | |
| 37 | |
| 38 **Input** | |
| 39 | |
| 40 There is no input necessary from the user. The tool connects to the Lambda-Miner database and uses the users login name to query it. | |
| 41 | |
| 42 **Output** | |
| 43 | |
| 44 CSV file containing the projects (id, name, sample count) corresponding to the user.]]> | |
| 45 </help> | |
| 46 <citations> | |
| 47 <citation type="doi">10.5194/egusphere-egu24-15782</citation> | |
| 48 </citations> | |
| 49 </tool> |