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comparison freebayes.xml @ 26:a028d13cd860 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
author iuc
date Thu, 04 May 2017 11:34:13 -0400
parents bf27106652f3
children 9f164587a92f
comparison
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25:bf27106652f3 26:a028d13cd860
1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-2"> 1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-3">
2 <description>bayesian genetic variant detector</description> 2 <description>bayesian genetic variant detector</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
33 #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": 33 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
34 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' 'input_variant_vcf.vcf.gz' && 34 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' 'input_variant_vcf.vcf.gz' &&
35 ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' && 35 ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' &&
36 #end if 36 #end if
37 37
38 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ): 38 ##if user has specified a region or target file, just use instead of calculating a set of unique regions
39 samtools view -H b_${bam_count}.bam | 39
40 grep "^@SQ" | 40 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
41 cut -f 2- | 41 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
42 awk '{ gsub("^SN:","",$1); 42 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
43 gsub("^LN:","",$2); 43 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
44 print $1"\t0\t"$2; }' >> regions_all.bed && 44 #else
45 #end for 45 ##divide up the regions in the bam file for efficient processing
46 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
47 samtools view -H b_${bam_count}.bam |
48 grep "^@SQ" |
49 cut -f 2- |
50 awk '{ gsub("^SN:","",$1);
51 gsub("^LN:","",$2);
52 print $1"\t0\t"$2; }' >> regions_all.bed &&
53 #end for
54 #end if
55
56
46 57
47 sort -u regions_all.bed > regions_uniq.bed && 58 sort -u regions_all.bed > regions_uniq.bed &&
48 ## split into even small chunks, this has some disatvantages and will not be used for the moment 59 ## split into even small chunks, this has some disatvantages and will not be used for the moment
49 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed && 60 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
50 61
70 #end for 81 #end for
71 --fasta-reference '${reference_fasta_filename}' 82 --fasta-reference '${reference_fasta_filename}'
72 83
73 ## Outputs 84 ## Outputs
74 --vcf './vcf_output/part_\$i.vcf' 85 --vcf './vcf_output/part_\$i.vcf'
75
76 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
77 --targets '${target_limit_type.input_target_bed}'
78 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
79 --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}'
80 #end if
81 86
82 ##advanced options 87 ##advanced options
83 #if str( $options_type.options_type_selector ) == "simple": 88 #if str( $options_type.options_type_selector ) == "simple":
84 ##do nothing as command like build up to this point is sufficinet for simple diploid calling 89 ##do nothing as command like build up to this point is sufficinet for simple diploid calling
85 90