Mercurial > repos > jjkoehorst > sapp

diff fasta2rdf.xml @ 35:fa736576c7ed draft

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planemo upload commit 16d0bc526ad02361a7c13231d4c50479c42d8d0f-dirty
author jjkoehorst
date Mon, 04 Jul 2016 10:37:59 -0400
parents f2cbf1230026
children
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--- a/fasta2rdf.xml	Wed Jun 29 02:21:47 2016 -0400
+++ b/fasta2rdf.xml	Mon Jul 04 10:37:59 2016 -0400
@@ -1,10 +1,9 @@
 <tool id="DFASTA2RDF" name="FASTA to RDF" version="0.1">
-	<description>SAPP - FASTA 2 RDF conversion</description>
+	<description></description>
 	<requirements>
 		<container type="docker">jjkoehorst/sappdocker:FASTA2RDF</container>
 	</requirements>
-
-	<command>java -jar /fasta2rdf/target/FASTA2RDF-0.1-jar-with-dependencies.jar
+	<command interpreter="docker">java -jar /fasta2rdf/FASTA2RDF-0.1-jar-with-dependencies.jar
                 '--type' '$source.fastaType' '--ignorestop' '$IgnoreStopCodon'
 		'--input' '$input' '--output' '$output' '-organism' '$organism'
 		'--ncbi_taxid' '$ncbi_taxid'
@@ -31,7 +30,8 @@
                                 <option value="genome"> Genome </option>
                                 <option value="gene"> Gene</option>
                                 <option value="protein"> Protein </option>
-                                <validator type="empty_field" message="Please select if it is a Genome, Gene or Protein" />
+                                <validator type="empty_field"
+                                        message="Please select if it is a Genome, Gene or Protein" />
                         </param>
                 </conditional>