Mercurial > repos > yhoogstrate > varscan_mpileup2snp_from_bam

changeset 51:11292b6c3c6c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author yhoogstrate
date Wed, 05 Mar 2014 08:47:37 -0500
parents cdc2a480cb1b
children b2dc8ab51a79
files samtools-parallel-mpileup.xml varscan_mpileup2snp.xml
diffstat 2 files changed, 4 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- 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" />
 			
--- 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>