diff create_features_from_gff3.xml @ 13:bb562d95b6cd draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7bf18c69becc57152efdadedf7ebd0bcfa382a15"

--- a/create_features_from_gff3.xml	Fri Apr 24 09:08:24 2020 -0400
+++ b/create_features_from_gff3.xml	Mon Jun 29 09:17:58 2020 -0400
@@ -15,16 +15,18 @@
 '$__user_email__'
 '$gff3_data'
 --source '${__app__.config.galaxy_infrastructure_url}/history/view/${__app__.security.encode_id($gff3_data.history_id)}'
+$use_name
+$disable_cds_recalculation
 
 > '$output']]></command>
   <inputs>
     <expand macro="org_or_guess" />
     <expand macro="gff3_input" />
+    <param name="use_name" type="boolean" truevalue="--user_name" falsevalue="" label="Use the given name instead of generating one" />
+    <param name="disable_cds_recalculation" type="boolean" truevalue="--disable_cds_recalculation" falsevalue="" label="Disable CDS recalculation and instead use the one provided" />
   </inputs>
   <outputs>
-	<data format="tabular" name="output" label="Process and Error Log">
-        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
-    </data>
+    <data format="txt" name="output" label="Process and Error Log"/>
   </outputs>
   <tests>
       <test>
@@ -33,20 +35,10 @@
               <param name="org_raw" value="Test org" />
           </conditional>
           <param name="gff3_data" value="merlin.gff"/>
-          <output name="output" file="load_gff3/output.tsv" compare="sim_size"/>
+          <output name="output" file="load_gff3/output.txt" compare="sim_size"/>
       </test>
   </tests>
   <help><![CDATA[
-**NOTA BENE**
-
-This is **incredibly, highly experimental**
-
-DO NOT:
-
--  Run on gff3 referencing multiple reference sequences/contigs
--  Expect it to work well
--  Expect it to work at all
-
 @REFERENCES@
 ]]></help>
   <expand macro="citations"/>