# HG changeset patch
# User devteam
# Date 1474811322 14400
# Node ID da6e10dee68b6836b74499afb399a83b2995b3e6
# Parent  52aed7d9ed2b94674cfe353e04d44a39054c53ec
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit ec3aa49a9d65ed3b69836c357e8a0278cd034a75

diff -r 52aed7d9ed2b -r da6e10dee68b freebayes.xml
--- a/freebayes.xml	Sun Sep 25 09:48:24 2016 -0400
+++ b/freebayes.xml	Sun Sep 25 09:48:42 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 ):