# HG changeset patch
# User yhoogstrate
# Date 1392652058 18000
# Node ID 2b6a44353622d4a4f6f95a3dcc10c636c5deb641
# Parent  af8a55f9dcc0244370a9bbbf2055d293a7c28042
Uploaded

diff -r af8a55f9dcc0 -r 2b6a44353622 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Mon Feb 17 10:42:46 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Mon Feb 17 10:47:38 2014 -0500
@@ -10,6 +10,7 @@
 			echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&2
 		#else
 		
+			<!-- Development stuff - might be useful for later
 			#if $reference_genome_source.source_select == "indexed_filtered"
 				echo "USED FASTA = $reference_genome_source.reference_genome"
 			#else if $reference_genome_source.source_select == "indexed_all"
@@ -17,16 +18,11 @@
 			#else if $reference_genome_source.source_select == "history"
 				echo "USED FASTA = $reference_genome_source.reference_genome"
 			#else
-				<!--
-					This is a workaround to obtain the "genome.fa" file that
-					corresponds to the dbkey of the alignments.
-					Because this file is "calculated" during run-time, it can
-					be used in a workflow.
-				-->
 				echo "USED FASTA = ${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
 			#end if
 			
 			;
+			-->
 			
 			samtools-mpileup-parallel mpileup
 				-t $samtools_threads
@@ -109,7 +105,7 @@
 		<!-- Find out how to access the reference genome from the BAM file(s) -->
 		<conditional name="reference_genome_source">
 			<param name="source_select" type="select" label="Fasta Source">
-				<option value="indexed_filtered">Use a built-in index (which fit your reference)</option>
+				<option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
 				<option value="history">Use reference from the history</option>
 				<option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option>
 				<option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>