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comparison bcftools_mpileup.xml @ 2:cf06b44624c7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:09:57 -0500
parents 12f7c5315f7f
children 4e1d23e5c691
comparison
equal deleted inserted replaced
1:9c711df3258d 2:cf06b44624c7
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description> 3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">mpileup</token> 5 <token name="@EXECUTABLE@">mpileup</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <xml name="bam_flag_options"> 7 <xml name="bam_flag_options">
14 <option value="64">Read is the first in a pair</option> 14 <option value="64">Read is the first in a pair</option>
15 <option value="128">Read is the second in a pair</option> 15 <option value="128">Read is the second in a pair</option>
16 <option value="256">The alignment or this read is not primary</option> 16 <option value="256">The alignment or this read is not primary</option>
17 <option value="512">The read fails platform/vendor quality checks</option> 17 <option value="512">The read fails platform/vendor quality checks</option>
18 <option value="1024">The read is a PCR or optical duplicate</option> 18 <option value="1024">The read is a PCR or optical duplicate</option>
19 </xml> 19 </xml>
20 </macros> 20 </macros>
21 <expand macro="requirements"> 21 <expand macro="requirements">
22 <expand macro="samtools_requirement"/> 22 <expand macro="samtools_requirement"/>
23 </expand> 23 </expand>
24 <expand macro="version_command" /> 24 <expand macro="version_command" />
35 #end if 35 #end if
36 #set $input_name = $input_base + '.' + $ext 36 #set $input_name = $input_base + '.' + $ext
37 #silent $bam_list.append($input_name) 37 #silent $bam_list.append($input_name)
38 ln -s '${input.input_bam}' ${input_name} && 38 ln -s '${input.input_bam}' ${input_name} &&
39 #if $input.input_bam.ext == 'bam': 39 #if $input.input_bam.ext == 'bam':
40 ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} && 40 ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
41 #else: 41 #else:
42 ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} && 42 ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} &&
43 #end if 43 #end if
44 #else: 44 #else:
45 #for $bam_count, $input_bam in enumerate( $input.input_bams ): 45 #for $bam_count, $input_bam in enumerate( $input.input_bams ):
46 #set $input_base = $re.sub('\W','_',$input_bam.display_name.replace('.bam','').replace('.cram','')) 46 #set $input_base = $re.sub('\W','_',$input_bam.display_name.replace('.bam','').replace('.cram',''))
47 #set $ext = 'bam' 47 #set $ext = 'bam'
57 #end for 57 #end for
58 #end if 58 #end if
59 59
60 #set $input_fa_ref = None 60 #set $input_fa_ref = None
61 #if $reference_source.reference_source_selector == "history": 61 #if $reference_source.reference_source_selector == "history":
62 #set $input_fa_ref = 'ref.fa' 62 #set $input_fa_ref = 'ref.fa'
63 ln -s '${reference_source.ref_file}' $input_fa_ref && 63 ln -s '${reference_source.ref_file}' $input_fa_ref &&
64 samtools faidx $input_fa_ref && 64 samtools faidx $input_fa_ref &&
65 #elif $reference_source.reference_source_selector == "cached": 65 #elif $reference_source.reference_source_selector == "cached":
66 #set $input_fa_ref = $reference_source.ref_file.fields.path 66 #set $input_fa_ref = $reference_source.ref_file.fields.path
67 #end if 67 #end if
68 68
69 #set $section = $sec_restrict 69 #set $section = $sec_restrict
70 @PREPARE_REGIONS_FILE@ 70 @PREPARE_REGIONS_FILE@
71 @PREPARE_TARGETS_FILE@ 71 @PREPARE_TARGETS_FILE@
79 #end if 79 #end if
80 80
81 ## Indel Calling section 81 ## Indel Calling section
82 #set $section = $sec_indel 82 #set $section = $sec_indel
83 #if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling': 83 #if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling':
84 --skip-indels 84 --skip-indels
85 #elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling': 85 #elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling':
86 -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}" 86 -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}"
87 -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}" 87 -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}"
88 -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}" 88 -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
89 -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}" 89 -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}"
90 -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}" 90 -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
91 --open-prob "${section.perform_indel_calling.open_seq_error_probability}" 91 --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
92 -F "${section.perform_indel_calling.minimum_gapped_read_fraction}" 92 -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
93 ${section.perform_indel_calling.gapped_read_per_sample} 93 ${section.perform_indel_calling.gapped_read_per_sample}
94 #if len( $section.perform_indel_calling.platform_list_repeat ): 94 #if len( $section.perform_indel_calling.platform_list_repeat ):
95 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }" 95 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
96 #end if 96 #end if
97 #end if 97 #end if
98 98
99 ## Filter section 99 ## Filter section
100 #set $section = $sec_filtering 100 #set $section = $sec_filtering
101 #if str( $section.filter_by_flags.filter_flags ) == "filter": 101 #if str( $section.filter_by_flags.filter_flags ) == "filter":
102 #if $section.filter_by_flags.require_flags: 102 #if $section.filter_by_flags.require_flags:
103 --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])} 103 --rf ${sum([int(flag) for flag in str($section.filter_by_flags.require_flags).split(',')])}
104 #end if 104 #end if
105 #if $section.filter_by_flags.exclude_flags: 105 #if $section.filter_by_flags.exclude_flags:
106 --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])} 106 --ff ${sum([int(flag) for flag in str($section.filter_by_flags.exclude_flags).split(',')])}
107 #end if 107 #end if
108 #end if 108 #end if
109 -d "${section.max_reads_per_bam}" 109 -d "${section.max_reads_per_bam}"
110 ${section.skip_anomalous_read_pairs} 110 ${section.skip_anomalous_read_pairs}
111 #if str( $section.quality.quality_settings ) == "adjust": 111 #if str( $section.quality.quality_settings ) == "adjust":
112 $section.quality.baq 112 $section.quality.baq
113 -q "${section.quality.minimum_mapping_quality}" 113 -q "${section.quality.minimum_mapping_quality}"
114 -Q "${section.quality.minimum_base_quality}" 114 -Q "${section.quality.minimum_base_quality}"
115 -C "${section.quality.coefficient_for_downgrading}" 115 -C "${section.quality.coefficient_for_downgrading}"
116 #end if 116 #end if
117 #if str( $section.read_groups.read_groups_selector ) == "ignore_rg": 117 #if str( $section.read_groups.read_groups_selector ) == "ignore_rg":
118 --ignore-RG 118 --ignore-RG
119 #elif str( $section.read_groups.read_groups_selector ) == "paste": 119 #elif str( $section.read_groups.read_groups_selector ) == "paste":
120 -G "${section.read_groups.rg_action}${read_groups_file}" 120 -G "${section.read_groups.rg_action}${read_groups_file}"
121 #elif str( $section.read_groups.read_groups_selector ) == "history" 121 #elif str( $section.read_groups.read_groups_selector ) == "history"
122 -G "${section.read_groups.rg_action}${section.read_groups.read_groups}" 122 -G "${section.read_groups.rg_action}${section.read_groups.read_groups}"
123 #end if 123 #end if
124 124
125 #set $section = $sec_output_options 125 #set $section = $sec_output_options
126 #if $section.output_tags: 126 #if $section.output_tags:
127 --annotate "$section.output_tags" 127 --annotate "$section.output_tags"
128 #end if 128 #end if
129 #if $section.gvcf: 129 #if $section.gvcf:
130 --gvcf "$section.gvcf" 130 --gvcf "$section.gvcf"
131 #end if 131 #end if
132 132
133 ## Subset section 133 ## Subset section
134 #set $section = $sec_subset 134 #set $section = $sec_subset
135 @SAMPLES@ 135 @SAMPLES@
145 145
146 ## Primary Input/Outputs 146 ## Primary Input/Outputs
147 #echo ' '.join($bam_list)# 147 #echo ' '.join($bam_list)#
148 > '$output_file' 148 > '$output_file'
149 #if str( $sec_filtering.read_groups.read_groups_selector ) == "paste": 149 #if str( $sec_filtering.read_groups.read_groups_selector ) == "paste":
150 && echo 'read-groups:' 150 && echo 'read-groups:'
151 && cat ${read_groups_file} 151 && cat ${read_groups_file}
152 #end if 152 #end if
153 ]]> 153 ]]></command>
154 </command>
155 <configfiles> 154 <configfiles>
156 <configfile name="read_groups_file"> 155 <configfile name="read_groups_file">
157 <![CDATA[#slurp 156 <![CDATA[#slurp
158 #set pasted_data = '' 157 #set pasted_data = ''
159 #set $section = $sec_filtering 158 #set $section = $sec_filtering
160 #if str( $section.read_groups.read_groups_selector ) == "paste": 159 #if str( $section.read_groups.read_groups_selector ) == "paste":
161 #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() ) 160 #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() )
162 #end if 161 #end if
163 #slurp 162 #slurp
164 ${pasted_data} 163 ${pasted_data}
165 ]]> 164 ]]>
166 </configfile> 165 </configfile>
442 @TARGETS_HELP@ 441 @TARGETS_HELP@
443 442
444 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 443 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
445 444
446 @BCFTOOLS_WIKI@ 445 @BCFTOOLS_WIKI@
447 ]]> 446 ]]></help>
448 </help>
449 <expand macro="citations" /> 447 <expand macro="citations" />
450 </tool> 448 </tool>