# HG changeset patch
# User yhoogstrate
# Date 1392740021 18000
# Node ID 3bb39a9058d97f1b84f393edbe0817ae46776427
# Parent  7946b09020e02f20790fbf7498c8da3795421bda
Uploaded

diff -r 7946b09020e0 -r 3bb39a9058d9 all_fasta.loc.sample
--- a/all_fasta.loc.sample	Tue Feb 18 05:29:59 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,18 +0,0 @@
-#This file lists the locations and dbkeys of all the fasta files
-#under the "genome" directory (a directory that contains a directory
-#for each build). The script extract_fasta.py will generate the file
-#all_fasta.loc. This file has the format (white space characters are
-#TAB characters):
-#
-#<unique_build_id>	<dbkey>		<display_name>	<file_path>
-#
-#So, all_fasta.loc could look something like this:
-#
-#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
-#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
-#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
-#
-#Your all_fasta.loc file should contain an entry for each individual
-#fasta file. So there will be multiple fasta files for each build,
-#such as with hg19 above.
-#
diff -r 7946b09020e0 -r 3bb39a9058d9 tool-data/all_fasta.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample	Tue Feb 18 11:13:41 2014 -0500
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
diff -r 7946b09020e0 -r 3bb39a9058d9 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Feb 18 11:13:41 2014 -0500
@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<table name="all_fasta" comment_char="#">
+	<columns>name, dbkey, display_name, value</columns>
+	<file path="tool-data/all_fasta.loc.sample" /> 
+</table>
\ No newline at end of file
diff -r 7946b09020e0 -r 3bb39a9058d9 varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Tue Feb 18 05:29:59 2014 -0500
+++ b/varscan_mpileup2snp_from_bam.xml	Tue Feb 18 11:13:41 2014 -0500
@@ -9,21 +9,6 @@
 		#if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
 			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!" >&amp;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"
-				echo "USED FASTA = $reference_genome_source.reference_genome"
-			#else if $reference_genome_source.source_select == "history"
-				echo "USED FASTA = $reference_genome_source.reference_genome"
-			#else
-				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
 				-f 
@@ -93,9 +78,9 @@
 					$varscan_variants
 			#end if
 			
-			$varscan_output_vcf
+			 --output-vcf $varscan_output_vcf
 			 
-			 > $output_table
+			 > $snv_output
 		#end if
 	</command>
 	
@@ -199,11 +184,15 @@
 			</when>
 		</conditional>
 		
-		<param type="boolean" name="varscan_output_vcf" falsevalue=" --output-vcf 0" truevalue=" --output-vcf 1" label="VarScan: If set to 1, outputs in VCF format" />
+		<param type="boolean" name="varscan_output_vcf" falsevalue="0" truevalue="1" label="VarScan: If set to 1, outputs in VCF format" />
 	</inputs>
 	
 	<outputs>
-		<data format="tabular" name="output_table" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
+		<data format="tabular" name="snv_output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}">
+			<change_format>
+				<when input="varscan_output_vcf" value="1" format="vcf" />
+			</change_format>
+		</data>
 	</outputs>
 	
 	<help>