Mercurial > repos > devteam > picard
diff picard_ValidateSamFile.xml @ 33:3f254c5ced1d draft default tip
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 |
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--- a/picard_ValidateSamFile.xml Mon Sep 25 08:32:17 2023 +0000 +++ b/picard_ValidateSamFile.xml Sun Mar 03 16:06:11 2024 +0000 @@ -1,14 +1,14 @@ -<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> - <description>assess validity of SAM/BAM dataset</description> - <macros> - <import>picard_macros.xml</import> - <token name="@WRAPPER_VERSION@">2</token> - </macros> - <expand macro="requirements" /> - <stdio> - <exit_code range="1:" level="warning"/> - </stdio> - <command><![CDATA[ +<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@"> + <description>assess validity of SAM/BAM dataset</description> + <macros> + <import>picard_macros.xml</import> + <token name="@WRAPPER_VERSION@">0</token> + </macros> + <expand macro="requirements"/> + <stdio> + <exit_code range="1:" level="warning"/> + </stdio> + <command><![CDATA[ ##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 @@ -21,148 +21,141 @@ #set $reference_fasta_filename = "localref.fa" #if str( $reference_source.reference_source_selector ) == "history": - ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + ln -sf '${reference_source.ref_file}' '${reference_fasta_filename}' && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if @java_options@ - picard - ValidateSamFile + picard ValidateSamFile - INPUT='$escaped_element_identifier' - OUTPUT="${outFile}" - MODE="${mode}" + --INPUT '$escaped_element_identifier' + --OUTPUT '${outFile}' + --MODE '${mode}' #if str( $ignore ) != "None": #for $element in str( $ignore ).split(','): ## See trello card https://trello.com/c/9nW02Zhd - IGNORE="${element}" + --IGNORE '${element}' #end for #end if - MAX_OUTPUT="${max_output}" - REFERENCE_SEQUENCE="${reference_fasta_filename}" - IGNORE_WARNINGS="${ignore_warnings}" - IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" - VALIDATE_INDEX="${validate_index}" - MAX_OPEN_TEMP_FILES=`ulimit -Sn` + --MAX_OUTPUT '${max_output}' + --REFERENCE_SEQUENCE '${reference_fasta_filename}' + --IGNORE_WARNINGS '${ignore_warnings}' + --IS_BISULFITE_SEQUENCED '${is_bisulfite_sequenced}' + --MAX_OPEN_TEMP_FILES `ulimit -Sn` - VERBOSITY=ERROR - QUIET=true + --VERBOSITY ERROR + --QUIET true ]]></command> - <inputs> - <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." /> - <conditional name="reference_source"> - <param name="reference_source_selector" type="select" label="Load reference genome from"> - <option value="cached">Local cache</option> - <option value="history">History</option> - </param> - <when value="cached"> - <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> - <options from_data_table="picard_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> + <inputs> + <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."/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> + <options from_data_table="picard_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available"/> + </options> + <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <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"/> + </when> + </conditional> + <param name="mode" type="select" label="Select output mode" help="MODE"> + <option value="VERBOSE">Verbose</option> + <option value="SUMMARY">Summary</option> </param> - </when> - <when value="history"> - <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" /> - </when> - </conditional> - - <param name="mode" type="select" label="Select output mode" help="MODE"> - <option value="VERBOSE">Verbose</option> - <option value="SUMMARY">Summary</option> - </param> - <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE"> - <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option> - <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option> - <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option> - <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option> - <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option> - <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option> - <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option> - <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option> - <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option> - <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option> - <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option> - <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option> - <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option> - <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option> - <option value="INVALID_CIGAR">INVALID_CIGAR</option> - <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option> - <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option> - <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option> - <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option> - <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option> - <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option> - <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option> - <option value="INVALID_TAG_NM">INVALID_TAG_NM</option> - <option value="MISSING_TAG_NM">MISSING_TAG_NM</option> - <option value="MISSING_HEADER">MISSING_HEADER</option> - <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option> - <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option> - <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option> - <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option> - <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option> - <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option> - <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option> - <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option> - <option value="TRUNCATED_FILE">TRUNCATED_FILE</option> - <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option> - <option value="EMPTY_READ">EMPTY_READ</option> - <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option> - <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option> - <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option> - <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option> - <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option> - <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option> - <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option> - <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option> - <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option> - <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option> - <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option> - <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option> - <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option> - <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option> - <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option> - <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option> - <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option> - <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option> - <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option> - <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option> - <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option> - </param> - <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/> - <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/> - <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"/> - <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"/> - - </inputs> - - <outputs> - <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/> - </outputs> - - <tests> - <test> - <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/> - <param name="reference_source_selector" value="history"/> - <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/> - <param name="mode" value="VERBOSE"/> - <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/> - <param name="max_output" value="100"/> - <param name="ignore_warnings" value="Fasle"/> - <param name="validate_index" value="True"/> - <param name="is_bisulfite_sequenced" value="False"/> - <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/> - </test> - </tests> - - <help> + <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE"> + <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option> + <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option> + <option value="INVALID_FLAG_MATE_UNMAPPED">INVALID_FLAG_MATE_UNMAPPED</option> + <option value="MISMATCH_FLAG_MATE_UNMAPPED">MISMATCH_FLAG_MATE_UNMAPPED</option> + <option value="INVALID_FLAG_MATE_NEG_STRAND">INVALID_FLAG_MATE_NEG_STRAND</option> + <option value="MISMATCH_FLAG_MATE_NEG_STRAND">MISMATCH_FLAG_MATE_NEG_STRAND</option> + <option value="INVALID_FLAG_FIRST_OF_PAIR">INVALID_FLAG_FIRST_OF_PAIR</option> + <option value="INVALID_FLAG_SECOND_OF_PAIR">INVALID_FLAG_SECOND_OF_PAIR</option> + <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND">PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND</option> + <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT">INVALID_FLAG_NOT_PRIM_ALIGNMENT</option> + <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT">INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT</option> + <option value="INVALID_FLAG_READ_UNMAPPED">INVALID_FLAG_READ_UNMAPPED</option> + <option value="INVALID_INSERT_SIZE">INVALID_INSERT_SIZE</option> + <option value="INVALID_MAPPING_QUALITY">INVALID_MAPPING_QUALITY</option> + <option value="INVALID_CIGAR">INVALID_CIGAR</option> + <option value="ADJACENT_INDEL_IN_CIGAR">ADJACENT_INDEL_IN_CIGAR</option> + <option value="INVALID_MATE_REF_INDEX">INVALID_MATE_REF_INDEX</option> + <option value="MISMATCH_MATE_REF_INDEX">MISMATCH_MATE_REF_INDEX</option> + <option value="INVALID_REFERENCE_INDEX">INVALID_REFERENCE_INDEX</option> + <option value="INVALID_ALIGNMENT_START">INVALID_ALIGNMENT_START</option> + <option value="MISMATCH_MATE_ALIGNMENT_START">MISMATCH_MATE_ALIGNMENT_START</option> + <option value="MATE_FIELD_MISMATCH">MATE_FIELD_MISMATCH</option> + <option value="INVALID_TAG_NM">INVALID_TAG_NM</option> + <option value="MISSING_TAG_NM">MISSING_TAG_NM</option> + <option value="MISSING_HEADER">MISSING_HEADER</option> + <option value="MISSING_SEQUENCE_DICTIONARY">MISSING_SEQUENCE_DICTIONARY</option> + <option value="MISSING_READ_GROUP">MISSING_READ_GROUP</option> + <option value="RECORD_OUT_OF_ORDER">RECORD_OUT_OF_ORDER</option> + <option value="READ_GROUP_NOT_FOUND">READ_GROUP_NOT_FOUND</option> + <option value="RECORD_MISSING_READ_GROUP">RECORD_MISSING_READ_GROUP</option> + <option value="INVALID_INDEXING_BIN">INVALID_INDEXING_BIN</option> + <option value="MISSING_VERSION_NUMBER">MISSING_VERSION_NUMBER</option> + <option value="INVALID_VERSION_NUMBER">INVALID_VERSION_NUMBER</option> + <option value="TRUNCATED_FILE">TRUNCATED_FILE</option> + <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH">MISMATCH_READ_LENGTH_AND_QUALS_LENGTH</option> + <option value="EMPTY_READ">EMPTY_READ</option> + <option value="CIGAR_MAPS_OFF_REFERENCE">CIGAR_MAPS_OFF_REFERENCE</option> + <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH">MISMATCH_READ_LENGTH_AND_E2_LENGTH</option> + <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH">MISMATCH_READ_LENGTH_AND_U2_LENGTH</option> + <option value="E2_BASE_EQUALS_PRIMARY_BASE">E2_BASE_EQUALS_PRIMARY_BASE</option> + <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK">BAM_FILE_MISSING_TERMINATOR_BLOCK</option> + <option value="UNRECOGNIZED_HEADER_TYPE">UNRECOGNIZED_HEADER_TYPE</option> + <option value="POORLY_FORMATTED_HEADER_TAG">POORLY_FORMATTED_HEADER_TAG</option> + <option value="HEADER_TAG_MULTIPLY_DEFINED">HEADER_TAG_MULTIPLY_DEFINED</option> + <option value="HEADER_RECORD_MISSING_REQUIRED_TAG">HEADER_RECORD_MISSING_REQUIRED_TAG</option> + <option value="INVALID_DATE_STRING">INVALID_DATE_STRING</option> + <option value="TAG_VALUE_TOO_LARGE">TAG_VALUE_TOO_LARGE</option> + <option value="INVALID_INDEX_FILE_POINTER">INVALID_INDEX_FILE_POINTER</option> + <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE">INVALID_PREDICTED_MEDIAN_INSERT_SIZE</option> + <option value="DUPLICATE_READ_GROUP_ID">DUPLICATE_READ_GROUP_ID</option> + <option value="MISSING_PLATFORM_VALUE">MISSING_PLATFORM_VALUE</option> + <option value="INVALID_PLATFORM_VALUE">INVALID_PLATFORM_VALUE</option> + <option value="DUPLICATE_PROGRAM_GROUP_ID">DUPLICATE_PROGRAM_GROUP_ID</option> + <option value="MATE_NOT_FOUND">MATE_NOT_FOUND</option> + <option value="MATES_ARE_SAME_END">MATES_ARE_SAME_END</option> + <option value="MISMATCH_MATE_CIGAR_STRING">MISMATCH_MATE_CIGAR_STRING</option> + <option value="MATE_CIGAR_STRING_INVALID_PRESENCE">MATE_CIGAR_STRING_INVALID_PRESENCE</option> + </param> + <param name="max_output" type="integer" value="100" label="The maximum number of lines output in verbose mode" help="MAX_OUTPUT; default=100"/> + <param name="ignore_warnings" type="boolean" label="If true, only report errors and ignore warnings" help="IGNORE_WARNINGS; default=False"/> + <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"/> + <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"/> + </inputs> + <outputs> + <data format="txt" name="outFile" label="${tool.name} on ${on_string}: BAM validation summary"/> + </outputs> + <tests> + <test> + <param name="inputFile" value="picard_ValidateSamFile.bam" ftype="bam"/> + <param name="reference_source_selector" value="history"/> + <param name="ref_file" value="picard_ValidateSamFile_ref.fa"/> + <param name="mode" value="VERBOSE"/> + <param name="ignore" value="INVALID_QUALITY_FORMAT,INVALID_FLAG_PROPER_PAIR"/> + <param name="max_output" value="100"/> + <param name="ignore_warnings" value="Fasle"/> + <param name="validate_index" value="True"/> + <param name="is_bisulfite_sequenced" value="False"/> + <output name="outFile" file="picard_ValidateSamFile_test1.txt" ftype="txt"/> + </test> + </tests> + <help> **Purpose** @@ -215,12 +208,12 @@ values: {true, false} IS_BISULFITE_SEQUENCED=Boolean - BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not + BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not counted as an error in computing the value of the NM tag. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} @more_info@ </help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>