diff flaimapper-gtf-from-fasta.xml @ 28:19d1402611ef draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty

--- a/flaimapper-gtf-from-fasta.xml	Sun Mar 29 05:32:04 2015 -0400
+++ b/flaimapper-gtf-from-fasta.xml	Wed Jun 03 07:27:47 2015 -0400
@@ -1,11 +1,18 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.1.5.b">
+<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w1">
 	<description>Extract GTF file from FASTA file (as FlaiMapper reference).</description>
 	<requirements>
-		<requirement type="package" version="0.8.2.1">pysam</requirement>
-		<requirement type="package" version="1.1.5">flaimapper</requirement>
+		<requirement type="package" version="1.2.1">flaimapper</requirement>
 	</requirements>
 	
+	<stdio>
+		<regex
+			match="[fai_load] build FASTA index." 
+			source="stderr" 
+			level="log" 
+			description="The FASTA file is being indexed." />
+	</stdio>
+	
 	<version_command>flaimapper --version</version_command>
 	
 	<command>
@@ -14,14 +21,6 @@
 			    $fasta
 	</command>
 	
-	<stdio>
-		<regex
-			match="[fai_load] build FASTA index." 
-			source="stderr" 
-			level="log" 
-			description="The FASTA file is being indexed." />
-	</stdio>
-	
 	<inputs>
 		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
 	</inputs>
@@ -32,9 +31,9 @@
 	
 	<tests>
 		<test>
-			<param name="fasta" value="ncrnadb09.fa" />
+			<param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" />
 			
-			<param name="output" value="ncrnadb09.gtf" />
+			<output name="output" file="test3/reference.gtf" />
 		</test>
 	</tests>