Mercurial > repos > gga > tripal_feature_sync
diff 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 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_sync.xml Mon Sep 11 05:53:20 2017 -0400 @@ -0,0 +1,77 @@ +<?xml version="1.0"?> +<tool id="feature_sync" profile="16.04" name="Synchronize features" version="@WRAPPER_VERSION@.0"> + <description>from Chado to Tripal</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <code file="tripal.py"/> + <expand macro="stdio"/> + <command><![CDATA[ + + @AUTH@ + + tripaille feature sync + + #for $rep in $repeat_types: + --types '${rep.types}' + #end for + + #for $rep in $repeat_ids: + --ids '${rep.ids}' + #end for + + --organism_id '${organism_id}' + + && + + echo "Data loaded" > $results + ]]></command> + <inputs> + <param argument="--organism_id" + type="select" + dynamic_options="list_organisms()" + label="Organism" /> + + <repeat name="repeat_types" title="Feature types"> + <param name="types" + argument="--types" + type="text" + optional="true" + label="Feature type to synchronize" + help="Type of records to be synced (e.g. 'gene' or 'mRNA')" /> + </repeat> + + <repeat name="repeat_ids" title="Feature ids"> + <param name="ids" + argument="--ids" + type="text" + optional="true" + label="Feature to synchronize" + help="Name of a feature to be synced (e.g. 'gene0001')" /> + </repeat> + </inputs> + <outputs> + <data format="txt" name="results" label="Synchronize features into Tripal" /> + </outputs> + <tests> + <test expect_failure="true"> + <param name="organism" value="Testus testus" /> + <param name="types" value="gene mRNA" /> + <param name="types" value="gene0001 gene0002" /> + + <expand macro="test_result" /> + </test> + </tests> + <help><![CDATA[ + @HELP_OVERVIEW@ + + **Synchronize Features** + + With this tool, you can synchronize some features from the Chado database into the Tripal instance. + A corresponding Drupal node will be created for each feature. + + @HELP@ + ]]></help> + <expand macro="citation"/> +</tool>