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comparison picard_ValidateSamFile.xml @ 24:e65f2d5fd3d8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
author iuc
date Sat, 15 Jan 2022 12:38:18 +0000
parents a5a13ea16d17
children fc3866ddc7b6
comparison
equal deleted inserted replaced
23:4740a2548206 24:e65f2d5fd3d8
78 <option value="SUMMARY">Summary</option> 78 <option value="SUMMARY">Summary</option>
79 </param> 79 </param>
80 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE"> 80 <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">
81 <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option> 81 <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>
82 <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option> 82 <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>
83 <option value="INVALID_FLAG_MATE_UNMAPPED"/> 83 <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option>
84 <option value="MISMATCH_FLAG_MATE_UNMAPPED"/> 84 <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option>
85 <option value="INVALID_FLAG_MATE_NEG_STRAND"/> 85 <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option>
86 <option value="MISMATCH_FLAG_MATE_NEG_STRAND"/> 86 <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option>
87 <option value="INVALID_FLAG_FIRST_OF_PAIR"/> 87 <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option>
88 <option value="INVALID_FLAG_SECOND_OF_PAIR"/> 88 <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option>
89 <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND"/> 89 <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option>
90 <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT"/> 90 <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option>
91 <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT"/> 91 <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option>
92 <option value="INVALID_FLAG_READ_UNMAPPED"/> 92 <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option>
93 <option value="INVALID_INSERT_SIZE"/> 93 <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option>
94 <option value="INVALID_MAPPING_QUALITY"/> 94 <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option>
95 <option value="INVALID_CIGAR"/> 95 <option value="INVALID_CIGAR">INVALID_CIGAR</option>
96 <option value="ADJACENT_INDEL_IN_CIGAR"/> 96 <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option>
97 <option value="INVALID_MATE_REF_INDEX"/> 97 <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option>
98 <option value="MISMATCH_MATE_REF_INDEX"/> 98 <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option>
99 <option value="INVALID_REFERENCE_INDEX"/> 99 <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option>
100 <option value="INVALID_ALIGNMENT_START"/> 100 <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option>
101 <option value="MISMATCH_MATE_ALIGNMENT_START"/> 101 <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option>
102 <option value="MATE_FIELD_MISMATCH"/> 102 <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option>
103 <option value="INVALID_TAG_NM"/> 103 <option value="INVALID_TAG_NM">INVALID_TAG_NM</option>
104 <option value="MISSING_TAG_NM"/> 104 <option value="MISSING_TAG_NM">MISSING_TAG_NM</option>
105 <option value="MISSING_HEADER"/> 105 <option value="MISSING_HEADER">MISSING_HEADER</option>
106 <option value="MISSING_SEQUENCE_DICTIONARY"/> 106 <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option>
107 <option value="MISSING_READ_GROUP"/> 107 <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option>
108 <option value="RECORD_OUT_OF_ORDER"/> 108 <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option>
109 <option value="READ_GROUP_NOT_FOUND"/> 109 <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option>
110 <option value="RECORD_MISSING_READ_GROUP"/> 110 <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option>
111 <option value="INVALID_INDEXING_BIN"/> 111 <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option>
112 <option value="MISSING_VERSION_NUMBER"/> 112 <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option>
113 <option value="INVALID_VERSION_NUMBER"/> 113 <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option>
114 <option value="TRUNCATED_FILE"/> 114 <option value="TRUNCATED_FILE">TRUNCATED_FILE</option>
115 <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH"/> 115 <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option>
116 <option value="EMPTY_READ"/> 116 <option value="EMPTY_READ">EMPTY_READ</option>
117 <option value="CIGAR_MAPS_OFF_REFERENCE"/> 117 <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option>
118 <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH"/> 118 <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option>
119 <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH"/> 119 <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option>
120 <option value="E2_BASE_EQUALS_PRIMARY_BASE"/> 120 <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option>
121 <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK"/> 121 <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option>
122 <option value="UNRECOGNIZED_HEADER_TYPE"/> 122 <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option>
123 <option value="POORLY_FORMATTED_HEADER_TAG"/> 123 <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option>
124 <option value="HEADER_TAG_MULTIPLY_DEFINED"/> 124 <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option>
125 <option value="HEADER_RECORD_MISSING_REQUIRED_TAG"/> 125 <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option>
126 <option value="INVALID_DATE_STRING"/> 126 <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option>
127 <option value="TAG_VALUE_TOO_LARGE"/> 127 <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option>
128 <option value="INVALID_INDEX_FILE_POINTER"/> 128 <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option>
129 <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE"/> 129 <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option>
130 <option value="DUPLICATE_READ_GROUP_ID"/> 130 <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option>
131 <option value="MISSING_PLATFORM_VALUE"/> 131 <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option>
132 <option value="INVALID_PLATFORM_VALUE"/> 132 <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option>
133 <option value="DUPLICATE_PROGRAM_GROUP_ID"/> 133 <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option>
134 <option value="MATE_NOT_FOUND"/> 134 <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option>
135 <option value="MATES_ARE_SAME_END"/> 135 <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option>
136 <option value="MISMATCH_MATE_CIGAR_STRING"/> 136 <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option>
137 <option value="MATE_CIGAR_STRING_INVALID_PRESENCE"/> 137 <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option>
138 </param> 138 </param>
139 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/> 139 <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/>
140 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/> 140 <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/>
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"/> 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"/>
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"/> 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"/>