| Previous changeset 23:52aed7d9ed2b (2016-09-25) Next changeset 25:bf27106652f3 (2017-02-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit ec3aa49a9d65ed3b69836c357e8a0278cd034a75 |
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modified:
freebayes.xml |
| b |
| 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 |
| b |
| @@ -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 ): |