Mercurial > repos > gga > tripal_feature_sync
comparison feature_sync.xml @ 0:c01c63c043f0 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 05:53:20 -0400 |
| parents | |
| children | e621d1187d73 |
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| -1:000000000000 | 0:c01c63c043f0 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="feature_sync" profile="16.04" name="Synchronize features" 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 feature sync | |
| 15 | |
| 16 #for $rep in $repeat_types: | |
| 17 --types '${rep.types}' | |
| 18 #end for | |
| 19 | |
| 20 #for $rep in $repeat_ids: | |
| 21 --ids '${rep.ids}' | |
| 22 #end for | |
| 23 | |
| 24 --organism_id '${organism_id}' | |
| 25 | |
| 26 && | |
| 27 | |
| 28 echo "Data loaded" > $results | |
| 29 ]]></command> | |
| 30 <inputs> | |
| 31 <param argument="--organism_id" | |
| 32 type="select" | |
| 33 dynamic_options="list_organisms()" | |
| 34 label="Organism" /> | |
| 35 | |
| 36 <repeat name="repeat_types" title="Feature types"> | |
| 37 <param name="types" | |
| 38 argument="--types" | |
| 39 type="text" | |
| 40 optional="true" | |
| 41 label="Feature type to synchronize" | |
| 42 help="Type of records to be synced (e.g. 'gene' or 'mRNA')" /> | |
| 43 </repeat> | |
| 44 | |
| 45 <repeat name="repeat_ids" title="Feature ids"> | |
| 46 <param name="ids" | |
| 47 argument="--ids" | |
| 48 type="text" | |
| 49 optional="true" | |
| 50 label="Feature to synchronize" | |
| 51 help="Name of a feature to be synced (e.g. 'gene0001')" /> | |
| 52 </repeat> | |
| 53 </inputs> | |
| 54 <outputs> | |
| 55 <data format="txt" name="results" label="Synchronize features into Tripal" /> | |
| 56 </outputs> | |
| 57 <tests> | |
| 58 <test expect_failure="true"> | |
| 59 <param name="organism" value="Testus testus" /> | |
| 60 <param name="types" value="gene mRNA" /> | |
| 61 <param name="types" value="gene0001 gene0002" /> | |
| 62 | |
| 63 <expand macro="test_result" /> | |
| 64 </test> | |
| 65 </tests> | |
| 66 <help><![CDATA[ | |
| 67 @HELP_OVERVIEW@ | |
| 68 | |
| 69 **Synchronize Features** | |
| 70 | |
| 71 With this tool, you can synchronize some features from the Chado database into the Tripal instance. | |
| 72 A corresponding Drupal node will be created for each feature. | |
| 73 | |
| 74 @HELP@ | |
| 75 ]]></help> | |
| 76 <expand macro="citation"/> | |
| 77 </tool> |