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comparison picard_ValidateSamFile.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
comparison
equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 <tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>assess validity of SAM/BAM dataset</description> 2 <description>assess validity of SAM/BAM dataset</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">2</token> 5 <token name="@WRAPPER_VERSION@">0</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <stdio> 8 <stdio>
9 <exit_code range="1:" level="warning"/> 9 <exit_code range="1:" level="warning"/>
10 </stdio> 10 </stdio>
11 <command><![CDATA[ 11 <command><![CDATA[
12 12
13 ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command 13 ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives 'unlimited' as output of `ulimit -Hn` command
14 14
15 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn` 15 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`
16 16
19 ##set up input files 19 ##set up input files
20 @symlink_element_identifier@ 20 @symlink_element_identifier@
21 #set $reference_fasta_filename = "localref.fa" 21 #set $reference_fasta_filename = "localref.fa"
22 22
23 #if str( $reference_source.reference_source_selector ) == "history": 23 #if str( $reference_source.reference_source_selector ) == "history":
24 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && 24 ln -sf '${reference_source.ref_file}' '${reference_fasta_filename}' &&
25 #else: 25 #else:
26 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) 26 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
27 #end if 27 #end if
28 28
29 @java_options@ 29 @java_options@
30 30
31 picard 31 picard ValidateSamFile
32 ValidateSamFile 32
33 33 --INPUT '$escaped_element_identifier'
34 INPUT='$escaped_element_identifier' 34 --OUTPUT '${outFile}'
35 OUTPUT="${outFile}" 35 --MODE '${mode}'
36 MODE="${mode}"
37 36
38 #if str( $ignore ) != "None": 37 #if str( $ignore ) != "None":
39 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd 38 #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd
40 IGNORE="${element}" 39 --IGNORE '${element}'
41 #end for 40 #end for
42 #end if 41 #end if
43 42
44 MAX_OUTPUT="${max_output}" 43 --MAX_OUTPUT '${max_output}'
45 REFERENCE_SEQUENCE="${reference_fasta_filename}" 44 --REFERENCE_SEQUENCE '${reference_fasta_filename}'
46 IGNORE_WARNINGS="${ignore_warnings}" 45 --IGNORE_WARNINGS '${ignore_warnings}'
47 IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" 46 --IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}'
48 VALIDATE_INDEX="${validate_index}" 47 --MAX_OPEN_TEMP_FILES `ulimit -Sn`
49 MAX_OPEN_TEMP_FILES=`ulimit -Sn` 48
50 49 --VERBOSITY ERROR
51 VERBOSITY=ERROR 50 --QUIET true
52 QUIET=true
53 51
54 ]]></command> 52 ]]></command>
55 <inputs> 53 <inputs>
56 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." /> 54 <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
57 <conditional name="reference_source"> 55 <conditional name="reference_source">
58 <param name="reference_source_selector" type="select" label="Load reference genome from"> 56 <param name="reference_source_selector" type="select" label="Load reference genome from">
59 <option value="cached">Local cache</option> 57 <option value="cached">Local cache</option>
60 <option value="history">History</option> 58 <option value="history">History</option>
61 </param> 59 </param>
62 <when value="cached"> 60 <when value="cached">
63 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> 61 <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">
64 <options from_data_table="picard_indexes"> 62 <options from_data_table="picard_indexes">
65 <filter type="sort_by" column="2" /> 63 <filter type="sort_by" column="2"/>
66 <validator type="no_options" message="No indexes are available" /> 64 <validator type="no_options" message="No indexes are available"/>
67 </options> 65 </options>
68 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> 66 <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>
67 </param>
68 </when>
69 <when value="history">
70 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command"/>
71 </when>
72 </conditional>
73 <param name="mode" type="select" label="Select output mode" help="MODE">
74 <option value="VERBOSE">Verbose</option>
75 <option value="SUMMARY">Summary</option>
69 </param> 76 </param>
70 </when> 77 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
71 <when value="history"> 78 <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>
72 <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> 79 <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>
73 </when> 80 <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option>
74 </conditional> 81 <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option>
75 82 <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option>
76 <param name="mode" type="select" label="Select output mode" help="MODE"> 83 <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option>
77 <option value="VERBOSE">Verbose</option> 84 <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option>
78 <option value="SUMMARY">Summary</option> 85 <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option>
79 </param> 86 <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option>
80 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE"> 87 <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option>
81 <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option> 88 <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option>
82 <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option> 89 <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option>
83 <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option> 90 <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option>
84 <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option> 91 <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option>
85 <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option> 92 <option value="INVALID_CIGAR">INVALID_CIGAR</option>
86 <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option> 93 <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option>
87 <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option> 94 <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option>
88 <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option> 95 <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option>
89 <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option> 96 <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option>
90 <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option> 97 <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option>
91 <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option> 98 <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option>
92 <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option> 99 <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option>
93 <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option> 100 <option value="INVALID_TAG_NM">INVALID_TAG_NM</option>
94 <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option> 101 <option value="MISSING_TAG_NM">MISSING_TAG_NM</option>
95 <option value="INVALID_CIGAR">INVALID_CIGAR</option> 102 <option value="MISSING_HEADER">MISSING_HEADER</option>
96 <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option> 103 <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option>
97 <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option> 104 <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option>
98 <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option> 105 <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option>
99 <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option> 106 <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option>
100 <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option> 107 <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option>
101 <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option> 108 <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option>
102 <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option> 109 <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option>
103 <option value="INVALID_TAG_NM">INVALID_TAG_NM</option> 110 <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option>
104 <option value="MISSING_TAG_NM">MISSING_TAG_NM</option> 111 <option value="TRUNCATED_FILE">TRUNCATED_FILE</option>
105 <option value="MISSING_HEADER">MISSING_HEADER</option> 112 <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option>
106 <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option> 113 <option value="EMPTY_READ">EMPTY_READ</option>
107 <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option> 114 <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option>
108 <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option> 115 <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option>
109 <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option> 116 <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option>
110 <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option> 117 <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option>
111 <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option> 118 <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option>
112 <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option> 119 <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option>
113 <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option> 120 <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option>
114 <option value="TRUNCATED_FILE">TRUNCATED_FILE</option> 121 <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option>
115 <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option> 122 <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option>
116 <option value="EMPTY_READ">EMPTY_READ</option> 123 <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option>
117 <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option> 124 <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option>
118 <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option> 125 <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option>
119 <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option> 126 <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option>
120 <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option> 127 <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option>
121 <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option> 128 <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option>
122 <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option> 129 <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option>
123 <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option> 130 <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option>
124 <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option> 131 <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option>
125 <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option> 132 <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option>
126 <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option> 133 <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option>
127 <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option> 134 <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option>
128 <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option> 135 </param>
129 <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option> 136 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
130 <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option> 137 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
131 <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option> 138 <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/>
132 <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option> 139 <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C-&gt;T is not counted as an error in computing the value of the NM tag; default=False"/>
133 <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option> 140 </inputs>
134 <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option> 141 <outputs>
135 <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option> 142 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/>
136 <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option> 143 </outputs>
137 <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option> 144 <tests>
138 </param> 145 <test>
139 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/> 146 <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
140 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/> 147 <param name="reference_source_selector" value="history"/>
141 <param name="validate_index" type="boolean" checked="True" label="If true and input is a BAM file with an index file, also validates the index" help="VALIDATE_INDEX; default=True"/> 148 <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/>
142 <param name="is_bisulfite_sequenced" type="boolean" label="Whether the SAM or BAM file consists of bisulfite sequenced reads" help="IS_BISULFITE_SEQUENCED; If so, C->T is not counted as an error in computing the value of the NM tag; default=False"/> 149 <param name="mode" value="VERBOSE"/>
143 150 <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/>
144 </inputs> 151 <param name="max_output" value="100"/>
145 152 <param name="ignore_warnings" value="Fasle"/>
146 <outputs> 153 <param name="validate_index" value="True"/>
147 <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/> 154 <param name="is_bisulfite_sequenced" value="False"/>
148 </outputs> 155 <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
149 156 </test>
150 <tests> 157 </tests>
151 <test> 158 <help>
152 <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/>
153 <param name="reference_source_selector" value="history"/>
154 <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/>
155 <param name="mode" value="VERBOSE"/>
156 <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/>
157 <param name="max_output" value="100"/>
158 <param name="ignore_warnings" value="Fasle"/>
159 <param name="validate_index" value="True"/>
160 <param name="is_bisulfite_sequenced" value="False"/>
161 <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/>
162 </test>
163 </tests>
164
165 <help>
166 159
167 **Purpose** 160 **Purpose**
168 161
169 Reads a SAM/BAM dataset and report on its validity. 162 Reads a SAM/BAM dataset and report on its validity.
170 163
213 VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default 206 VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default
214 value: true. This option can be set to 'null' to clear the default value. Possible 207 value: true. This option can be set to 'null' to clear the default value. Possible
215 values: {true, false} 208 values: {true, false}
216 209
217 IS_BISULFITE_SEQUENCED=Boolean 210 IS_BISULFITE_SEQUENCED=Boolean
218 BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not 211 BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C-&gt;T is not
219 counted as an error in computing the value of the NM tag. Default value: false. This 212 counted as an error in computing the value of the NM tag. Default value: false. This
220 option can be set to 'null' to clear the default value. Possible values: {true, false} 213 option can be set to 'null' to clear the default value. Possible values: {true, false}
221 214
222 @more_info@ 215 @more_info@
223 216
224 </help> 217 </help>
225 <expand macro="citations" /> 218 <expand macro="citations"/>
226 </tool> 219 </tool>