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comparison freebayes.xml @ 24:da6e10dee68b draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit ec3aa49a9d65ed3b69836c357e8a0278cd034a75
author devteam
date Sun, 25 Sep 2016 09:48:42 -0400
parents 52aed7d9ed2b
children bf27106652f3
comparison
equal deleted inserted replaced
23:52aed7d9ed2b 24:da6e10dee68b
14 ##set up input files 14 ##set up input files
15 15
16 #set $reference_fasta_filename = "localref.fa" 16 #set $reference_fasta_filename = "localref.fa"
17 17
18 #if str( $reference_source.reference_source_selector ) == "history": 18 #if str( $reference_source.reference_source_selector ) == "history":
19 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && 19 ln -s -f "${reference_source.ref_file}" "${reference_fasta_filename}" &&
20 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 && 20 samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
21 #else: 21 #else:
22 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 22 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
23 #end if 23 #end if
24 24
25 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): 25 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
26 ln -s "${input_bam}" "b_${bam_count}.bam" && 26 ln -s -f "${input_bam}" "b_${bam_count}.bam" &&
27 ln -s "${input_bam.metadata.bam_index}" "b_${bam_count}.bam.bai" && 27 ln -s -f "${input_bam.metadata.bam_index}" "b_${bam_count}.bam.bai" &&
28 #end for 28 #end for
29 29
30 ## Tabixize optional input_varinat_vcf file (for --variant-input option) 30 ## Tabixize optional input_varinat_vcf file (for --variant-input option)
31 #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": 31 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
32 ln -s "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" && 32 ln -s -f "${options_type.optional_inputs.input_variant_type.input_variant_vcf}" "input_variant_vcf.vcf.gz" &&
33 ln -s "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" && 33 ln -s -f "${Tabixized_input}" "input_variant_vcf.vcf.gz.tbi" &&
34 #end if 34 #end if
35 35
36 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): 36 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
37 samtools view -H b_${bam_count}.bam | grep "^@SQ" | cut -f 2- | awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed && 37 samtools view -H b_${bam_count}.bam | grep "^@SQ" | cut -f 2- | awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
38 #end for 38 #end for