diff flaimapper.xml @ 8:c5df479c423b draft

Uploaded

--- a/flaimapper.xml	Fri Nov 07 10:54:58 2014 -0500
+++ b/flaimapper.xml	Thu Mar 19 10:17:46 2015 -0400
@@ -1,39 +1,39 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.1.0">
+<tool id="flaimapper" name="FlaiMapper" version="1.1.2.a">
 	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
 	<requirements>
-		<requirement type="package" version="1.1.0">flaimapper</requirement>
 		<requirement type="package" version="0.7.7">pysam</requirement>
+		<requirement type="package" version="0.8.1">pysam</requirement>
+		<requirement type="package" version="1.1.2">flaimapper</requirement>
 	</requirements>
+	
+	<version_command>flaimapper --version</version_command>
+	
 	<command>
-		##rm $mask".tbi"
-		##rm $fasta".fai"
-		
 		flaimapper
 			 -v
 			 -f $output_format
 			 -o $output
 			 -m $mask
 			 -r $fasta
-			#for $alignment in $alignments
-				$alignment
-			#end for
+		
+		#for $alignment in $alignments
+			$alignment
+		#end for
 	</command>
 	
-	<version_command>flaimapper --version</version_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="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 -->
+		<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>
 	</inputs>
 	
@@ -42,6 +42,8 @@
 	</outputs>
 	
 	<help>
+		You must have 'easy_install' installed.
+		
 		FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data
 		
 		doi:10.1093/bioinformatics/btu696