# HG changeset patch
# User yhoogstrate
# Date 1394027257 18000
# Node ID 11292b6c3c6c785b923bd361acd82d370555a8b1
# Parent  cdc2a480cb1bfeca82220df12754b33e1954b22f
Uploaded

diff -r cdc2a480cb1b -r 11292b6c3c6c samtools-parallel-mpileup.xml
--- a/samtools-parallel-mpileup.xml	Wed Mar 05 08:03:59 2014 -0500
+++ b/samtools-parallel-mpileup.xml	Wed Mar 05 08:47:37 2014 -0500
@@ -182,7 +182,7 @@
 	
 	<tests>
 		<test><!-- Use classical samtools -->
-			<param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" />
+			<param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" />
 			<param name="reference_genome_source.source_select" value="attribute" />
 			<param name="extended_parameters_regions.samtools_regions" value="entire_genome" />
 			
@@ -195,7 +195,7 @@
 			<output name="output" file="hg19_mutant.mpileup" /> 
 		</test>
 		<test><!-- Use parallelized samtools -->
-			<param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" />
+			<param name="alignments" value="hg19_mutant.bam.txt" dbkey="hg19" ftype="bam" />
 			<param name="reference_genome_source.source_select" value="attribute" />
 			<param name="extended_parameters_regions.samtools_regions" value="entire_genome" />
 			
diff -r cdc2a480cb1b -r 11292b6c3c6c varscan_mpileup2snp.xml
--- a/varscan_mpileup2snp.xml	Wed Mar 05 08:03:59 2014 -0500
+++ b/varscan_mpileup2snp.xml	Wed Mar 05 08:47:37 2014 -0500
@@ -28,7 +28,7 @@
 	</command>
 	
 	<inputs>
-		<param format="mpileup" multiple="true" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/>
+		<param format="mpileup" name="mpileup_input" type="data" label="Alignment file" help="Mapped reads in BAM or SAM format."/>
 		
 		<conditional name="extended_parameters">
 			<param name="parameters" type="select" label="VarScan parameters" help="For more advanced VarScan settings.">
@@ -53,7 +53,7 @@
 	</inputs>
 	
 	<outputs>
-		<data format="tabular" name="snv_output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}">
+		<data format="tabular" name="snv_output" label="${tool.name} on ${mpileup_input.hid}: ${mpileup_input.name}">
 			<change_format>
 				<when input="varscan_output_vcf" value="1" format="vcf" />
 			</change_format>