Mercurial > repos > bvalot > pymlst
comparison clamlst_import.xml @ 0:a3cc35af3635 draft
planemo upload for repository https://github.com/bvalot/pyMLST commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb
| author | bvalot |
|---|---|
| date | Thu, 16 Jun 2022 12:32:28 +0000 |
| parents | |
| children | 5b2c48fa0175 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:a3cc35af3635 |
|---|---|
| 1 <tool id="clamlst_import_wrapper" name="Import MLST database" version="2.1.3"> | |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.1.3">pymlst</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" level="fatal" /> | |
| 8 </stdio> | |
| 9 <version_command>claMLST -v</version_command> | |
| 10 <command> | |
| 11 claMLST import --force --no-prompt | |
| 12 #if $mlst | |
| 13 -m $mlst | |
| 14 #end if | |
| 15 $database '$search' &> $logfile | |
| 16 </command> | |
| 17 <inputs> | |
| 18 <param name="search" type="text" value="" optional="false" size="50" | |
| 19 label="Species name to import" | |
| 20 help="Bacterial species to download from pubMLST database" /> | |
| 21 <param name="mlst" type="text" value="" optional="true" size="50" | |
| 22 label="MLST shema" | |
| 23 help="Precise mlst shema if multiple exists for the " /> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data name="logfile" format="txt" label="${tool.name} import on ${search}: log" /> | |
| 27 <data name="database" format="sqlite" label="claMLST database on ${search}" /> | |
| 28 </outputs> | |
| 29 <tests> | |
| 30 <test expect_num_outputs="2"> | |
| 31 <param name="search" value="Escherichia spp" /> | |
| 32 <param name="mlst" value="achtman" /> | |
| 33 <output name="logfile" ftype="txt"> | |
| 34 <assert_contents> | |
| 35 <has_text text="One element found : escherichia spp" /> | |
| 36 <has_text text="One element found : mlst (achtman)" /> | |
| 37 <has_text text="Database initialized" /> | |
| 38 </assert_contents> | |
| 39 </output> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help> | |
| 43 **What it does** | |
| 44 | |
| 45 Import a classical MLST database from pubMLST | |
| 46 Example : | |
| 47 - Pseudomonas aeruginosa | |
| 48 - Escherichia spp (mlst=achtman) | |
| 49 | |
| 50 **License and citation** | |
| 51 | |
| 52 This Galaxy tool is Copyright © 2022 `B. Valot` and is released under the `GPL3 license`. | |
| 53 </help> | |
| 54 <citations> | |
| 55 </citations> | |
| 56 </tool> |