Mercurial > repos > devteam > freebayes

changeset 5:0f44dd2e7fe3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit ec3aa49a9d65ed3b69836c357e8a0278cd034a75
author devteam
date Sun, 25 Sep 2016 09:48:28 -0400
parents c171daf263dd
children 3aacf7637e02
files freebayes.xml
diffstat 1 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/freebayes.xml	Sun Sep 25 09:48:11 2016 -0400
+++ b/freebayes.xml	Sun Sep 25 09:48:28 2016 -0400
@@ -16,21 +16,21 @@
     #set $reference_fasta_filename = "localref.fa"
 
     #if str( $reference_source.reference_source_selector ) == "history":
-        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
+        ln -s -f "${reference_source.ref_file}" "${reference_fasta_filename}" &&
         samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
     #else:
         #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
     #end if
 
     #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
-        ln -s "${input_bam}" "b_${bam_count}.bam" &&
-        ln -s "${input_bam.metadata.bam_index}" "b_${bam_count}.bam.bai" &&
+        ln -s -f "${input_bam}" "b_${bam_count}.bam" &&
+        ln -s -f "${input_bam.metadata.bam_index}" "b_${bam_count}.bam.bai" &&
     #end for
 
     ## Tabixize optional input_varinat_vcf file (for --variant-input option)
     #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
-        ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &&
-        ln -s "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &&
+        ln -s -f "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &&
+        ln -s -f "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &&
     #end if
 
     #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):