Mercurial > repos > devteam > picard
comparison picard_ValidateSamFile.xml @ 24:e65f2d5fd3d8 draft
"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 |
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| 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"/> |