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comparison samtools_mpileup.xml @ 6:483949f5c3b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:15:58 -0400
parents 5872c9894a37
children edbe9587b15d
comparison
equal deleted inserted replaced
5:9b8d98f0e6b2 6:483949f5c3b0
1 <tool id="samtools_mpileup" name="MPileup" version="2.1.1"> 1 <tool id="samtools_mpileup" name="MPileup" version="2.1.3">
2 <description>call variants</description> 2 <description>multi-way pileup of variants</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command><![CDATA[
10 <![CDATA[ 10 #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):
11 ln -s '${input_bam}' 'localbam_${bam_count}.bam' &&
12 ln -s '${input_bam.metadata.bam_index}' 'localbam_${bam_count}.bam.bai' &&
13 #end for
14
11 #if $reference_source.reference_source_selector == "history": 15 #if $reference_source.reference_source_selector == "history":
12 ln -s "${reference_source.ref_file}" && samtools faidx `basename "${reference_source.ref_file}"` && samtools mpileup 16 ln -s '${reference_source.ref_file}' &&
17 samtools faidx `basename '${reference_source.ref_file}'` &&
18 #end if
19
20 samtools mpileup
21 #if $reference_source.reference_source_selector != "history":
22 -f '${reference_source.ref_file.fields.path}'
13 #else: 23 #else:
14 samtools mpileup 24 -f '${reference_source.ref_file}'
15 #end if 25 #end if
16 #if $reference_source.reference_source_selector != "history": 26 #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):
17 -f "${reference_source.ref_file.fields.path}" 27 localbam_${bam_count}.bam
18 #else:
19 -f "${reference_source.ref_file}"
20 #end if
21 #for $bam in $reference_source.input_bam:
22 "${bam}"
23 #end for 28 #end for
24 #if str( $advanced_options.advanced_options_selector ) == "advanced": 29 #if str( $advanced_options.advanced_options_selector ) == "advanced":
25 #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter": 30 #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":
26 #if $advanced_options.filter_by_flags.require_flags: 31 #if $advanced_options.filter_by_flags.require_flags:
27 --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])} 32 --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])}
29 #if $advanced_options.filter_by_flags.exclude_flags: 34 #if $advanced_options.filter_by_flags.exclude_flags:
30 --ff ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.exclude_flags).split(',')])} 35 --ff ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.exclude_flags).split(',')])}
31 #end if 36 #end if
32 #end if 37 #end if
33 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste": 38 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
34 -l "$pasted_regions" 39 -l '$pasted_regions'
35 #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history" 40 #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"
36 -l "$advanced_options.limit_by_region.bed_regions" 41 -l '$advanced_options.limit_by_region.bed_regions'
37 #end if 42 #end if
38 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste": 43 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
39 -G "$excluded_read_groups" 44 -G '$excluded_read_groups'
40 #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history" 45 #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
41 -G "$advanced_options.exclude_read_group.read_groups" 46 -G '$advanced_options.exclude_read_group.read_groups'
42 #end if 47 #end if
43 ${advanced_options.skip_anomalous_read_pairs} 48 ${advanced_options.skip_anomalous_read_pairs}
44 ${advanced_options.disable_probabilistic_realignment} 49 ${advanced_options.disable_probabilistic_realignment}
45 -C "${advanced_options.coefficient_for_downgrading}" 50 -C ${advanced_options.coefficient_for_downgrading}
46 -d "${advanced_options.max_reads_per_bam}" 51 -d ${advanced_options.max_reads_per_bam}
47 ${advanced_options.extended_BAQ_computation} 52 ${advanced_options.extended_BAQ_computation}
48 -q "${advanced_options.minimum_mapping_quality}" 53 -q ${advanced_options.minimum_mapping_quality}
49 -Q "${advanced_options.minimum_base_quality}" 54 -Q ${advanced_options.minimum_base_quality}
50 #if str( $advanced_options.region_string ): 55 #if str( $advanced_options.region_string ):
51 -r "${advanced_options.region_string}" 56 -r '${advanced_options.region_string}'
52 #end if 57 #end if
53
54 #end if 58 #end if
55 #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation': 59 #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation':
56 ##
57
58 ${genotype_likelihood_computation_type.output_format} 60 ${genotype_likelihood_computation_type.output_format}
59 ${genotype_likelihood_computation_type.compressed} 61 ${genotype_likelihood_computation_type.compressed}
60 62
61 #if str( $genotype_likelihood_computation_type.output_tags ) != "None": 63 #if str( $genotype_likelihood_computation_type.output_tags ) != "None":
62 --output-tags "${genotype_likelihood_computation_type.output_tags}" 64 --output-tags '${genotype_likelihood_computation_type.output_tags}'
63 #end if 65 #end if
64 66
65 #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling': 67 #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling':
66 -o "${genotype_likelihood_computation_type.perform_indel_calling.gap_open_sequencing_error_probability}" 68 --open-prob ${genotype_likelihood_computation_type.perform_indel_calling.gap_open_sequencing_error_probability}
67 -e "${genotype_likelihood_computation_type.perform_indel_calling.gap_extension_sequencing_error_probability}" 69 -e ${genotype_likelihood_computation_type.perform_indel_calling.gap_extension_sequencing_error_probability}
68 -h "${genotype_likelihood_computation_type.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}" 70 -h ${genotype_likelihood_computation_type.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}
69 -L "${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}" 71 -L ${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}
70 -m "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}" 72 -m ${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}
71 --open-prob "${genotype_likelihood_computation_type.perform_indel_calling.open_seq_error_probability}" 73 -F ${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_read_fraction}
72 -F "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_read_fraction}"
73 ${genotype_likelihood_computation_type.perform_indel_calling.gapped_read_per_sample} 74 ${genotype_likelihood_computation_type.perform_indel_calling.gapped_read_per_sample}
74 #if len( $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ): 75 #if len( $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ):
75 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ] ) }" 76 -P '${ ",".join( str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ) }'
76 #end if 77 #end if
77 #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling': 78 #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling':
78 -I 79 -I
79 #end if 80 #end if
80
81
82 #else: 81 #else:
83 ${genotype_likelihood_computation_type.base_position_on_reads} 82 ${genotype_likelihood_computation_type.base_position_on_reads}
84 ${genotype_likelihood_computation_type.output_mapping_quality} 83 ${genotype_likelihood_computation_type.output_mapping_quality}
85 #end if 84 #end if
86 --output "$output_mpileup" 2> "$output_log" 85 --output '$output_mpileup'
87 ]]> 86 ]]></command>
88 </command> 87
88 <configfiles>
89 <configfile name="excluded_read_groups"><![CDATA[
90 #set pasted_data = ''
91 #if str( $advanced_options.advanced_options_selector ) == "advanced":
92 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
93 #set pasted_data = '\t'.join( str( $advanced_options.exclude_read_group['read_groups'] ).split() )
94 #end if
95 #end if
96 ${pasted_data}
97 ]]></configfile>
98 <configfile name="pasted_regions"><![CDATA[
99 #set pasted_data = ''
100 #if str( $advanced_options.advanced_options_selector ) == "advanced":
101 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
102 #set pasted_data = '\t'.join( str( $advanced_options.limit_by_region['region_paste'] ).split() )
103 #end if
104 #end if
105 ${pasted_data}
106 ]]></configfile>
107 </configfiles>
108
89 <inputs> 109 <inputs>
90 <conditional name="reference_source"> 110 <conditional name="reference_source">
91 <param label="Choose the source for the reference genome" name="reference_source_selector" type="select"> 111 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
92 <option value="cached">Use a built-in genome</option> 112 <option value="cached">Use a built-in genome</option>
93 <option value="history">Use a genome from the history</option> 113 <option value="history">Use a genome from the history</option>
94 </param> 114 </param>
95 <when value="cached"> 115 <when value="cached">
96 <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True"> 116 <param name="input_bam" type="data" format="bam" multiple="True" min="1" label="BAM file(s)">
97 <validator type="unspecified_build" /> 117 <validator type="unspecified_build" />
98 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" /> 118 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
99 </param> 119 </param>
100 <param label="Using reference genome" name="ref_file" type="select"> 120 <param name="ref_file" type="select" label="Using reference genome">
101 <options from_data_table="fasta_indexes" /> 121 <options from_data_table="fasta_indexes" />
102 </param> 122 </param>
103 </when> 123 </when>
104 <when value="history"> 124 <when value="history">
105 <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True"> 125 <param name="input_bam" type="data" format="bam" multiple="True" min="1" label="BAM file(s)">
106 <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" /> 126 <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
107 </param> 127 </param>
108 <param format="fasta" label="Using reference genome" name="ref_file" type="data" /> 128 <param name="ref_file" type="data" format="fasta" label="Using reference genome" />
109 </when> 129 </when>
110 </conditional> 130 </conditional>
111 <conditional name="genotype_likelihood_computation_type"> 131 <conditional name="genotype_likelihood_computation_type">
112 <param label="Genotype Likelihood Computation" name="genotype_likelihood_computation_type_selector" type="select"> 132 <param name="genotype_likelihood_computation_type_selector" type="select" label="Genotype Likelihood Computation">
113 <option selected="True" value="perform_genotype_likelihood_computation">Perform genotype likelihood computation (--VCF, --BCF options)</option> 133 <option selected="True" value="perform_genotype_likelihood_computation">Perform genotype likelihood computation (--VCF, --BCF options)</option>
114 <option value="do_not_perform_genotype_likelihood_computation">Do not perform genotype likelihood computation (output pileup)</option> 134 <option value="do_not_perform_genotype_likelihood_computation">Do not perform genotype likelihood computation (output pileup)</option>
115 </param> 135 </param>
116 <when value="perform_genotype_likelihood_computation"> 136 <when value="perform_genotype_likelihood_computation">
117 <param label="Choose the output format" name="output_format" type="select"> 137 <param name="output_format" type="select" label="Choose the output format">
118 <option value="--VCF">VCF</option> 138 <option value="--VCF">VCF</option>
119 <option value="--BCF">BCF</option> 139 <option value="--BCF">BCF</option>
120 </param> 140 </param>
121 <param checked="False" falsevalue="--uncompressed" label="Compress output" name="compressed" truevalue="" type="boolean" help="--incompressed; default=False"/> 141 <param name="compressed" argument="--uncompressed" type="boolean" truevalue="" falsevalue="--uncompressed" checked="False" label="Compress output" />
122 <param name="output_tags" optional="True" type="select" multiple="True" display="checkboxes" label="Optional tags to output" help="--output-tags"> 142 <param name="output_tags" argument="--output-tags" type="select" optional="True" multiple="True" display="checkboxes" label="Optional tags to output">
123 <option value="DP">DP (Number of high-quality bases)</option> 143 <option value="DP">DP (Number of high-quality bases)</option>
124 <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option> 144 <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option>
125 <option value="DV">DV (Number of high-quality non-reference bases)</option> 145 <option value="DV">DV (Number of high-quality non-reference bases)</option>
126 <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option> 146 <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option>
127 <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option> 147 <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option>
128 <option value="SP">SP (Phred-scaled strand bias P-value)</option> 148 <option value="SP">SP (Phred-scaled strand bias P-value)</option>
129 </param> 149 </param>
130 <conditional name="perform_indel_calling"> 150 <conditional name="perform_indel_calling">
131 <param label="Perform INDEL calling" name="perform_indel_calling_selector" type="select"> 151 <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling">
132 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option> 152 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option>
133 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option> 153 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option>
134 <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option> 154 <option value="do_not_perform_indel_calling">Do not perform INDEL calling (-I)</option>
135 </param> 155 </param>
136 <when value="perform_indel_calling_def" /> 156 <when value="perform_indel_calling_def" />
137 <when value="perform_indel_calling"> 157 <when value="perform_indel_calling">
138 <param label="Phred-scaled gap open sequencing error probability" name="gap_open_sequencing_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/> 158 <param name="gap_open_sequencing_error_probability" argument="--open-prob" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="Reducing this value leads to more indel calls" />
139 <param label="Phred-scaled gap extension sequencing error probability" name="gap_extension_sequencing_error_probability" type="integer" value="20" help="--ext-prob; Reducing this value leads to longer indels. default=20"/> 159 <param name="gap_extension_sequencing_error_probability" argument="--ext-prob" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" help="Reducing this value leads to longer indels" />
140 <param label="Coefficient for modeling homopolymer errors." name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" help="--tandem-qual; default=100"/> 160 <param name="coefficient_for_modeling_homopolymer_errors" argument="--tandem-qual" type="integer" value="100" label="Coefficient for modeling homopolymer errors" />
141 <param label="Skip INDEL calling if the average per-sample depth is above" name="skip_indel_calling_above_sample_depth" type="integer" value="250" help="--max-idepth; default=250"/> 161 <param name="skip_indel_calling_above_sample_depth" argument="--max-idepth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" />
142 <param label="Minimum gapped reads for indel candidates" name="minimum_gapped_reads_for_indel_candidates" type="integer" value="1" help="--min-ireads; default=1"/> 162 <param name="minimum_gapped_reads_for_indel_candidates" argument="--min-ireads" type="integer" value="1" label="Minimum gapped reads for indel candidates" />
143 <param label="Phred-scaled gap open sequencing error probability" name="open_seq_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/> 163 <param name="minimum_gapped_read_fraction" argument="--gap-frac" type="float" value="0.002" label="Minimum fraction of gapped reads" />
144 <param label="Minimum fraction of gapped reads" name="minimum_gapped_read_fraction" type="float" value="0.002" help="--gap-frac; default=0.002"/> 164 <param name="gapped_read_per_sample" argument="--per-sample-mF" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Apply --min-ireads and --gap-frac values on a per-sample basis" help="By default both options are applied to reads pooled from all samples"/>
145 <param checked="False" falsevalue="" label="Apply --min-ireads and --gap-frac values on a per-sample basis" name="gapped_read_per_sample" truevalue="-p" type="boolean" help="--per-sample-mF; by default both options are applied to reads pooled from all samples"/> 165 <repeat name="platform_list_repeat" title="Platform for INDEL candidates" help="--platforms">
146 <repeat name="platform_list_repeat" title="Platform for INDEL candidates"> 166 <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
147 <param label="Platform to use for INDEL candidates" name="platform_entry" type="text" value="" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
148 </repeat> 167 </repeat>
149 </when> 168 </when>
150 <when value="do_not_perform_indel_calling" /> 169 <when value="do_not_perform_indel_calling" />
151 </conditional> 170 </conditional>
152 171
153 </when> 172 </when>
154 <when value="do_not_perform_genotype_likelihood_computation"> 173 <when value="do_not_perform_genotype_likelihood_computation">
155 <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/> 174 <param name="base_position_on_reads" argument="--output-BP" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Output base positions on reads" />
156 <param checked="False" falsevalue="" label="Output mapping quality" name="output_mapping_quality" truevalue="-s" type="boolean" help="--output-MQ"/> 175 <param name="output_mapping_quality" argument="--output-MQ" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output mapping quality" />
157 </when> 176 </when>
158 </conditional> 177 </conditional>
159 <conditional name="advanced_options"> 178 <conditional name="advanced_options">
160 <param label="Set advanced options" name="advanced_options_selector" type="select"> 179 <param name="advanced_options_selector" type="select" label="Set advanced options">
161 <option selected="True" value="basic">Basic</option> 180 <option selected="True" value="basic">Basic</option>
162 <option value="advanced">Advanced</option> 181 <option value="advanced">Advanced</option>
163 </param> 182 </param>
183 <when value="basic" />
164 <when value="advanced"> 184 <when value="advanced">
165 <conditional name="filter_by_flags"> 185 <conditional name="filter_by_flags">
166 <param label="Set filter by flags" name="filter_flags" type="select"> 186 <param name="filter_flags" type="select" label="Set filter by flags">
167 <option selected="True" value="nofilter">Do not filter</option> 187 <option selected="True" value="nofilter">Do not filter</option>
168 <option value="filter">Filter by flags to exclude or require</option> 188 <option value="filter">Filter by flags to exclude or require</option>
169 </param> 189 </param>
170 <when value="filter"> 190 <when value="filter">
171 <param display="checkboxes" label="Require" multiple="True" name="require_flags" type="select" help="--incl-flags"> 191 <param name="require_flags" argument="--incl-flags" type="select" multiple="True" display="checkboxes" label="Require">
172 <option value="1">Read is paired</option> 192 <option value="1">Read is paired</option>
173 <option value="2">Read is mapped in a proper pair</option> 193 <option value="2">Read is mapped in a proper pair</option>
174 <option value="4">The read is unmapped</option> 194 <option value="4">The read is unmapped</option>
175 <option value="8">The mate is unmapped</option> 195 <option value="8">The mate is unmapped</option>
176 <option value="16">Read strand</option> 196 <option value="16">Read strand</option>
179 <option value="128">Read is the second in a pair</option> 199 <option value="128">Read is the second in a pair</option>
180 <option value="256">The alignment or this read is not primary</option> 200 <option value="256">The alignment or this read is not primary</option>
181 <option value="512">The read fails platform/vendor quality checks</option> 201 <option value="512">The read fails platform/vendor quality checks</option>
182 <option value="1024">The read is a PCR or optical duplicate</option> 202 <option value="1024">The read is a PCR or optical duplicate</option>
183 </param> 203 </param>
184 <param display="checkboxes" label="Exclude" multiple="True" name="exclude_flags" type="select" help="--excl-flags"> 204 <param name="exclude_flags" argument="--excl-flags" type="select" multiple="True" display="checkboxes" label="Exclude">
185 <option value="1">Read is paired</option> 205 <option value="1">Read is paired</option>
186 <option value="2">Read is mapped in a proper pair</option> 206 <option value="2">Read is mapped in a proper pair</option>
187 <option value="4">The read is unmapped</option> 207 <option value="4">The read is unmapped</option>
188 <option value="8">The mate is unmapped</option> 208 <option value="8">The mate is unmapped</option>
189 <option value="16">Read strand</option> 209 <option value="16">Read strand</option>
196 </param> 216 </param>
197 </when> 217 </when>
198 <when value="nofilter" /> 218 <when value="nofilter" />
199 </conditional> 219 </conditional>
200 <conditional name="limit_by_region"> 220 <conditional name="limit_by_region">
201 <param label="Select regions to call" name="limit_by_regions" type="select"> 221 <param name="limit_by_regions" argument="--positions" type="select" label="Select regions to call">
202 <option selected="True" value="no_limit">Do not limit</option> 222 <option selected="True" value="no_limit">Do not limit</option>
203 <option value="history">From an uploaded BED file (--positions)</option> 223 <option value="history">From a BED file</option>
204 <option value="paste">Paste a list of regions or BED (--region)</option> 224 <option value="paste">Paste a list of regions or BED</option>
205 </param> 225 </param>
206 <when value="history"> 226 <when value="history">
207 <param format="bed" label="BED file" name="bed_regions" type="data" help="--positions"> 227 <param name="bed_regions" type="data" format="bed" label="BED file">
208 <validator type="dataset_ok_validator" /> 228 <validator type="dataset_ok_validator" />
209 </param> 229 </param>
210 </when> 230 </when>
211 <when value="paste"> 231 <when value="paste">
212 <param area="true" help="Paste a list of regions in BED format or as a list of chromosomes and positions" label="Regions" name="region_paste" size="10x35" type="text"/> 232 <param name="region_paste" type="text" area="true" size="10x35" label="Regions" help="Paste a list of regions in BED format or as a list of chromosomes and positions" />
213 </when> 233 </when>
214 <when value="no_limit" /> 234 <when value="no_limit" />
215 </conditional> 235 </conditional>
216 <conditional name="exclude_read_group"> 236 <conditional name="exclude_read_group">
217 <param label="Select read groups to exclude" name="exclude_read_groups" type="select" help="--exclude-RG"> 237 <param name="exclude_read_groups" argument="--exclude-RG" type="select" label="Select read groups to exclude">
218 <option selected="True" value="no_limit">Do not exclude</option> 238 <option selected="True" value="no_limit">Do not exclude</option>
219 <option value="history">From an uploaded text file</option> 239 <option value="history">From a text file</option>
220 <option value="paste">Paste a list of read groups</option> 240 <option value="paste">Paste a list of read groups</option>
221 </param> 241 </param>
222 <when value="history"> 242 <when value="history">
223 <param format="txt" label="Text file" name="read_groups" type="data"> 243 <param name="read_groups" type="data" format="txt" label="Text file">
224 <validator type="dataset_ok_validator" /> 244 <validator type="dataset_ok_validator" />
225 </param> 245 </param>
226 </when> 246 </when>
227 <when value="paste"> 247 <when value="paste">
228 <param area="true" help="Paste a list of read groups" label="Read groups" name="group_paste" size="10x35" type="text" /> 248 <param name="group_paste" type="text" area="true" size="10x35" label="Read groups" help="Paste a list of read groups" />
229 </when> 249 </when>
230 <when value="no_limit" /> 250 <when value="no_limit" />
231 </conditional> 251 </conditional>
232 <param checked="False" falsevalue="" label="Disable read-pair overlap detection" name="ignore_overlaps" truevalue="-x" type="boolean" help="--ignore-overlaps"/> 252 <param name="ignore_overlaps" argument="--ignore-overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" />
233 <param checked="False" falsevalue="" label="Do not skip anomalous read pairs in variant calling" name="skip_anomalous_read_pairs" truevalue="-A" type="boolean" help="--count-orphans"/> 253 <param name="skip_anomalous_read_pairs" argument="--count-orphans" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" />
234 <param checked="False" falsevalue="" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" name="disable_probabilistic_realignment" truevalue="-B" type="boolean" help="--no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments"/> 254 <param name="disable_probabilistic_realignment" argument="--no-BAQ" type="boolean" truevalue="-B" falsevalue="" checked="False" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" help="BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments" />
235 <param label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" name="coefficient_for_downgrading" type="integer" value="0" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/> 255 <param name="coefficient_for_downgrading" argument="--adjust-MQ" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" help="Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50" />
236 <param label="Max reads per BAM" max="1024" min="1" name="max_reads_per_bam" type="integer" value="250" help="--max-depth; default=250"/> 256 <param name="max_reads_per_bam" argument="--max-depth" type="integer" max="1024" min="1" value="250" label="Max reads per BAM" />
237 <param checked="False" falsevalue="" label="Redo BAQ computation" name="extended_BAQ_computation" truevalue="-E" type="boolean" help="--redo-BAQ; ignore existing BQ tags"/> 257 <param name="extended_BAQ_computation" argument="--redo-BAQ" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Redo BAQ computation" help="Ignore existing BQ tags" />
238 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/> 258 <param name="minimum_mapping_quality" argument="--min-MQ" type="integer" value="0" label="Minimum mapping quality for an alignment to be used" />
239 <param label="Minimum base quality for a base to be considered" name="minimum_base_quality" type="integer" value="13" help="--min-BQ; default=13"/> 259 <param name="minimum_base_quality" argument="--min-BQ" type="integer" value="13" label="Minimum base quality for a base to be considered" />
240 <param label="Only generate pileup in region" name="region_string" type="text" value="" help="--region; If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" /> 260 <param name="region_string" argument="--region" type="text" value="" label="Only generate pileup in region" help="If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" />
241 </when> 261 </when>
242 <when value="basic" />
243 </conditional> 262 </conditional>
244 </inputs> 263 </inputs>
245 <outputs> 264 <outputs>
246 <data format="pileup" label="${tool.name} on ${on_string}" name="output_mpileup"> 265 <data name="output_mpileup" format="pileup" label="${tool.name} on ${on_string}">
247 <change_format> 266 <change_format>
248 <when format="bcf" input="genotype_likelihood_computation_type.output_format" value="--BCF" /> 267 <when format="bcf" input="genotype_likelihood_computation_type.output_format" value="--BCF" />
249 <when format="vcf" input="genotype_likelihood_computation_type.output_format" value="--VCF" /> 268 <when format="vcf" input="genotype_likelihood_computation_type.output_format" value="--VCF" />
250 </change_format> 269 </change_format>
251 </data> 270 </data>
252 <data format="txt" label="${tool.name} on ${on_string} (log)" name="output_log" />
253 </outputs> 271 </outputs>
254 <tests> 272 <tests>
255 <test> 273 <test>
256 <param name="reference_source_selector" value="history" /> 274 <param name="reference_source_selector" value="history" />
257 <param ftype="fasta" name="ref_file" value="phiX.fasta" /> 275 <param name="ref_file" ftype="fasta" value="phiX.fasta" />
258 <param ftype="bam" name="input_bam" value="samtools_mpileup_in_1.bam" /> 276 <param name="input_bam" ftype="bam" value="samtools_mpileup_in_1.bam" />
259 <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" /> 277 <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" />
260 <param name="advanced_options_selector" value="basic" /> 278 <param name="advanced_options_selector" value="basic" />
261 <param name="base_position_on_reads" value="true" /> 279 <param name="base_position_on_reads" value="true" />
262 <param name="output_mapping_quality" value="true" /> 280 <param name="output_mapping_quality" value="true" />
263 <output file="samtools_mpileup_out_1.pileup" name="output_mpileup" /> 281 <output name="output_mpileup" file="samtools_mpileup_out_1.pileup" />
264 <output file="samtools_mpileup_out_1.log" name="output_log" />
265 </test> 282 </test>
266 <test> 283 <test>
267 <param name="reference_source_selector" value="history" /> 284 <param name="reference_source_selector" value="history" />
268 <param ftype="fasta" name="ref_file" value="phiX.fasta" /> 285 <param name="ref_file" ftype="fasta" value="phiX.fasta" />
269 <param ftype="bam" name="input_bam" value="phiX.bam" /> 286 <param name="input_bam" ftype="bam" value="phiX.bam" />
270 <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" /> 287 <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" />
271 <param name="gap_extension_sequencing_error_probability" value="20" /> 288 <param name="gap_extension_sequencing_error_probability" value="20" />
272 <param name="coefficient_for_modeling_homopolymer_errors" value="100" /> 289 <param name="coefficient_for_modeling_homopolymer_errors" value="100" />
273 <param name="perform_indel_calling_selector" value="perform_indel_calling" /> 290 <param name="perform_indel_calling_selector" value="perform_indel_calling" />
274 <param name="skip_indel_calling_above_sample_depth" value="250" /> 291 <param name="skip_indel_calling_above_sample_depth" value="250" />
275 <param name="gap_open_sequencing_error_probability" value="40" /> 292 <param name="gap_open_sequencing_error_probability" value="40" />
276 <param name="platform_list_repeat" value="0" /> 293 <param name="platform_list_repeat" value="0" />
277 <param name="advanced_options_selector" value="basic" /> 294 <param name="advanced_options_selector" value="basic" />
278 <param name="genotype_likelihood_computation_type|output_format" value="VCF" /> 295 <param name="genotype_likelihood_computation_type|output_format" value="VCF" />
279 <output file="samtools_mpileup_out_2.vcf" ftype="vcf" lines_diff="8" name="output_mpileup" /> 296 <output name="output_mpileup" file="samtools_mpileup_out_2.vcf" ftype="vcf" lines_diff="8" />
280 <output file="samtools_mpileup_out_2.log" name="output_log" /> 297 </test>
298 <test>
299 <param name="reference_source_selector" value="history" />
300 <param name="ref_file" ftype="fasta" value="phiX.fasta" />
301 <param name="input_bam" ftype="bam" value="samtools_mpileup_in_1.bam" />
302 <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" />
303 <param name="advanced_options_selector" value="advanced" />
304 <param name="minimum_base_quality" value="0" /><!-- most reads have ultra low quality resuling in empty columns -->
305 <param name="base_position_on_reads" value="true" />
306 <param name="output_mapping_quality" value="true" />
307 <output name="output_mpileup" file="samtools_mpileup_out_3.pileup" />
281 </test> 308 </test>
282 </tests> 309 </tests>
283 <help> 310 <help><![CDATA[
284 <![CDATA[
285 **What it does** 311 **What it does**
286 312
287 Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample. 313 Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines.
288 314 If sample identifiers are absent, each input file is regarded as one sample.
289 ------
290
291 **Input options**::
292
293 -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding
294 -A, --count-orphans do not discard anomalous read pairs
295 -b, --bam-list FILE list of input BAM filenames, one per line
296 -B, --no-BAQ disable BAQ (per-Base Alignment Quality)
297 -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0]
298 -d, --max-depth INT max per-BAM depth; avoids excessive memory usage [250]
299 -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs
300 -f, --fasta-ref FILE faidx indexed reference sequence file
301 -G, --exclude-RG FILE exclude read groups listed in FILE
302 -l, --positions FILE skip unlisted positions (chr pos) or regions (BED)
303 -q, --min-MQ INT skip alignments with mapQ smaller than INT [0]
304 -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [13]
305 -r, --region REG region in which pileup is generated
306 -R, --ignore-RG ignore RG tags (one BAM = one sample)
307 --rf, --incl-flags STR|INT required flags: skip reads with mask bits unset []
308 --ff, --excl-flags STR|INT filter flags: skip reads with mask bits set
309 [UNMAP,SECONDARY,QCFAIL,DUP]
310 -x, --ignore-overlaps disable read-pair overlap detection
311
312 **Output options**::
313
314 -o, --output FILE write output to FILE [standard output]
315 -g, --BCF generate genotype likelihoods in BCF format
316 -v, --VCF generate genotype likelihoods in VCF format
317
318 **Output options for mpileup format** (without -g/-v)::
319
320 -O, --output-BP output base positions on reads
321 -s, --output-MQ output mapping quality
322
323 **Output options for genotype likelihoods** (when -g/-v is used)::
324
325 -t, --output-tags LIST optional tags to output: DP,DPR,DV,DP4,INFO/DPR,SP []
326 -u, --uncompressed generate uncompressed VCF/BCF output
327
328 **SNP/INDEL genotype likelihoods options** (effective with -g/-v)::
329
330 -e, --ext-prob INT Phred-scaled gap extension seq error probability [20]
331 -F, --gap-frac FLOAT minimum fraction of gapped reads [0.002]
332 -h, --tandem-qual INT coefficient for homopolymer errors [100]
333 -I, --skip-indels do not perform indel calling
334 -L, --max-idepth INT maximum per-sample depth for INDEL calling [250]
335 -m, --min-ireads INT minimum number gapped reads for indel candidates [1]
336 -o, --open-prob INT Phred-scaled gap open seq error probability [40]
337 -p, --per-sample-mF apply -m and -F per-sample for increased sensitivity
338 -P, --platforms STR comma separated list of platforms for indels [all]
339 315
340 **Notes**: Assuming diploid individuals. 316 **Notes**: Assuming diploid individuals.
341 ]]> 317 ]]></help>
342 </help>
343 <configfiles>
344 <configfile name="excluded_read_groups">
345 <![CDATA[
346 #set pasted_data = ''
347 #if str( $advanced_options.advanced_options_selector ) == "advanced":
348 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
349 #set pasted_data = '\t'.join( str( $advanced_options.exclude_read_group['read_groups'] ).split() )
350 #end if
351 #end if
352 ${pasted_data}
353 ]]>
354 </configfile>
355 <configfile name="pasted_regions">
356 <![CDATA[
357 #set pasted_data = ''
358 #if str( $advanced_options.advanced_options_selector ) == "advanced":
359 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
360 #set pasted_data = '\t'.join( str( $advanced_options.limit_by_region['region_paste'] ).split() )
361 #end if
362 #end if
363 ${pasted_data}
364 ]]>
365 </configfile>
366 </configfiles>
367 <expand macro="citations" /> 318 <expand macro="citations" />
368 </tool> 319 </tool>