# HG changeset patch
# User yhoogstrate
# Date 1402476775 14400
# Node ID bd5fd2f82f3c0a556a69c4b5790325cb75b4616c
# Parent  f89704ed1d8faed5575c2fa6a33aa323e4cb776d
Uploaded

diff -r f89704ed1d8f -r bd5fd2f82f3c varscan_mpileup2snp.xml
--- a/varscan_mpileup2snp.xml	Tue Jun 10 10:42:22 2014 -0400
+++ b/varscan_mpileup2snp.xml	Wed Jun 11 04:52:55 2014 -0400
@@ -21,8 +21,8 @@
 				 $varscan_variants 
 		#end if
 		
-		#if $varscan_output_vcf
-			 --output-vcf 1 
+		#if $varscan_output == "vcf"
+		 --output-vcf 1 
 		#end if
 		
 		 2> stderr.txt 
@@ -52,13 +52,16 @@
 			</when>
 		</conditional>
 		
-		<param type="boolean" name="varscan_output_vcf" falsevalue="0" truevalue="1"  label="VarScan: If set to 1, outputs in VCF format" />
+		<param name="varscan_output" type="select" label="Output format">
+			<option value="vcf">VCF</option>
+			<option value="tabular">tabular</option>
+		</param>
 	</inputs>
 	
 	<outputs>
 		<data format="tabular" name="snv_output" label="${tool.name} on ${mpileup_input.hid}: ${mpileup_input.name}">
 			<change_format>
-				<when input="varscan_output_vcf" value="1" format="vcf" />
+				<when input="varscan_output" value="vcf" format="vcf" />
 			</change_format>
 		</data>
 	</outputs>
@@ -69,7 +72,6 @@
 			<param name="parameters" value="default" />
 			<param name="varscan_output_vcf" value="1" />
 			
-			
 			<output name="snv_output" file="hg19_mutant.vcf" />
 		</test>
 	</tests>
diff -r f89704ed1d8f -r bd5fd2f82f3c varscan_mpileup2snp_from_bam.xml
--- a/varscan_mpileup2snp_from_bam.xml	Tue Jun 10 10:42:22 2014 -0400
+++ b/varscan_mpileup2snp_from_bam.xml	Wed Jun 11 04:52:55 2014 -0400
@@ -79,7 +79,7 @@
 			#end for
 			 2>stderr_1.txt
 			
-			#if $sort_mpileup
+			#if $mpileup_parallelization.sort_mpileup
 			 | sort -k 1,1 -k 2,2 
 			#end if
 			
@@ -99,7 +99,7 @@
 					 $varscan_variants 
 			#end if
 			
-			#if $varscan_output_vcf
+			#if $varscan_output == "vcf"
 			 --output-vcf 1 
 			#end if
 			
@@ -132,10 +132,10 @@
 				<option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>
 			</param>
 			<when value="history">
-				<param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (fasta)" help="Reference genome (genome.fa) that corresponds to the *.bam file." />
+				<param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (FASTA)" help="Reference genome (genome.fa) that corresponds to the *.bam file." />
 			</when>
 			<when value="indexed_filtered">
-				<param name="reference_genome" type="select" label="Reference Genome used during alignment (fasta)" >
+				<param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" >
 					<options from_data_table="all_fasta">
 						<column name="name"  index="2"/>
 						<column name="dbkey" index="1"/>
@@ -146,7 +146,7 @@
 				</param>
 			</when>
 			<when value="indexed_all">
-				<param name="reference_genome" type="select" label="Reference Genome used during alignment (fasta)" >
+				<param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" >
 					<options from_data_table="all_fasta">
 						<column name="name"  index="2"/>
 						<column name="dbkey" index="1"/>
@@ -167,7 +167,7 @@
 			</param>
 			<when value="entire_genome" />
 			<when value="region">
-				<param type="text" name="samtools_r" label="Samtools: region in which pileup is generated" help="chr:pos or chr:start-end" />
+				<param type="text" name="samtools_r" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:pos or chr:start-end" />
 			</when>
 			<when value="regions_file_pos">
 				<param type="data" name="samtools_l" format="tabular" label="Samtools: list of positions (chr pos)" />
@@ -185,11 +185,10 @@
 			<when value="false" />
 			<when value="true">
 				<param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" />
+				<param name="sort_mpileup" type="boolean" truevalue="true" falsevalue="false" label="Sort mpileup file (SLOW)" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." />
 			</when>
 		</conditional>
 		
-		<param name="sort_mpileup" type="boolean" truevalue="true" falsevalue="false" label="Sort mpileup file" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." />
-		
 		<conditional name="extended_parameters">
 			<param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings.">
 				<option value="default">Default settings</option>
@@ -229,13 +228,16 @@
 			</when>
 		</conditional>
 		
-		<param type="boolean" name="varscan_output_vcf" falsevalue="0" truevalue="1"  label="VarScan: If set to 1, outputs in VCF format" />
+		<param name="varscan_output" type="select" label="Output format">
+			<option value="vcf">VCF</option>
+			<option value="tabular">tabular</option>
+		</param>
 	</inputs>
 	
 	<outputs>
 		<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" />
+				<when input="varscan_output" value="vcf" format="vcf" />
 			</change_format>
 		</data>
 	</outputs>