Mercurial > repos > yhoogstrate > flaimapper

changeset 2:83c9552188d1 draft

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Uploaded
author yhoogstrate
date Fri, 07 Nov 2014 10:17:38 -0500
parents 5035af9394d1
children 83bf9e65cc10
files flaimapper.xml
diffstat 1 files changed, 6 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/flaimapper.xml	Fri Nov 07 09:37:14 2014 -0500
+++ b/flaimapper.xml	Fri Nov 07 10:17:38 2014 -0500
@@ -6,6 +6,9 @@
 		<requirement type="package" version="0.7.7">pysam</requirement>
 	</requirements>
 	<command>
+		##rm $mask".tbi"
+		##rm $fasta".fai"
+		
 		flaimapper
 			 -v
 			 -f $output_format
@@ -22,14 +25,14 @@
 		
 		<param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
 		
-		<param name="output_format" type="select" label="Get">
+		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
+		
+		<param name="output_format" type="select" label="Output format">
 			<option value="1">Tabular (1 fragment per column)</option>
 			<option value="2">Tabular  (1 precursor per column)</option>
 			<option value="3">GenBank</option>
 			<!-- option value="gtf">GTF/GFF</option -->
 		</param>
-		
-		<param name="fasta" type="data" format="fa,fasta" label="Fasta sequence corresponding to reference genome" help="" />
 	</inputs>
 	
 	<outputs>