diff flaimapper.xml @ 18:0e9520cf7587 draft

Uploaded

--- a/flaimapper.xml	Fri Mar 20 06:33:35 2015 -0400
+++ b/flaimapper.xml	Fri Mar 20 10:45:21 2015 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.1.2.d">
+<tool id="flaimapper" name="FlaiMapper" version="1.1.4.a">
 	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
 	<requirements>
 		<requirement type="package" version="0.8.2.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! -->
-		<requirement type="package" version="1.1.2">flaimapper</requirement>
+		<requirement type="package" version="1.1.4">flaimapper</requirement>
 	</requirements>
 	
 	<version_command>flaimapper --version</version_command>
@@ -19,18 +19,12 @@
 		#for $alignment in $alignments
 			$alignment
 		#end for
-		
-		2&gt; stderr.txt ; 
-		
-		grep -v '[fai_load] build FASTA index.' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
-		
-		cat stderr.txt >&amp;2
 	</command>
 	
 	<inputs>
 		<param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
 		
-		<param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
+		<param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
 			
 		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />