Mercurial > repos > gga > tripal_organism_sync
comparison organism_sync.xml @ 0:98e917aa6819 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit f745b23c84a615bf434d717c8c0e553a012f0268
| author | gga |
|---|---|
| date | Mon, 11 Sep 2017 05:54:11 -0400 |
| parents | |
| children | 5d45a37e5e9b |
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| -1:000000000000 | 0:98e917aa6819 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="organism_sync" profile="16.04" name="Synchronize an organism" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>from Chado to Tripal</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <code file="tripal.py"/> | |
| 9 <expand macro="stdio"/> | |
| 10 <command><![CDATA[ | |
| 11 | |
| 12 @AUTH@ | |
| 13 | |
| 14 tripaille organism sync | |
| 15 | |
| 16 --organism_id '${organism_id}' | |
| 17 | |
| 18 && | |
| 19 | |
| 20 echo "Data loaded" > $results | |
| 21 ]]></command> | |
| 22 <inputs> | |
| 23 <param argument="--organism_id" | |
| 24 type="select" | |
| 25 dynamic_options="list_organisms()" | |
| 26 label="Organism" /> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data format="txt" name="results" label="Synchronize Organism into Tripal" /> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test expect_failure="true"> | |
| 33 <param name="organism_id" value="Testus testus" /> | |
| 34 | |
| 35 <expand macro="test_result" /> | |
| 36 </test> | |
| 37 </tests> | |
| 38 <help><![CDATA[ | |
| 39 @HELP_OVERVIEW@ | |
| 40 | |
| 41 **Synchronize Organism** | |
| 42 | |
| 43 With this tool, you can synchronize an organism from the Chado database into the Tripal instance. | |
| 44 A corresponding Drupal node will be created. | |
| 45 | |
| 46 @HELP@ | |
| 47 ]]></help> | |
| 48 <expand macro="citation"/> | |
| 49 </tool> |