Mercurial > repos > devteam > picard
view picard_ValidateSamFile.xml @ 10:126c30841c38 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit f65b40f4eb3c3431b8d9213f86238deebfd6bc29
author | devteam |
---|---|
date | Thu, 08 Dec 2016 06:43:24 -0500 |
parents | 41b8d087a2d2 |
children | 486d7500da69 |
line wrap: on
line source
<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.0"> <description>assess validity of SAM/BAM dataset</description> <macros> <import>picard_macros.xml</import> </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 [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn` && ##set up input files @symlink_element_identifier@ #set $reference_fasta_filename = "localref.fa" #if str( $reference_source.reference_source_selector ) == "history": ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && #else: #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) #end if @java_options@ picard ValidateSamFile INPUT='$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}" #end for #end if 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 ]]></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"/> </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"/> <option value="MISMATCH_FLAG_MATE_UNMAPPED"/> <option value="INVALID_FLAG_MATE_NEG_STRAND"/> <option value="MISMATCH_FLAG_MATE_NEG_STRAND"/> <option value="INVALID_FLAG_FIRST_OF_PAIR"/> <option value="INVALID_FLAG_SECOND_OF_PAIR"/> <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND"/> <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT"/> <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT"/> <option value="INVALID_FLAG_READ_UNMAPPED"/> <option value="INVALID_INSERT_SIZE"/> <option value="INVALID_MAPPING_QUALITY"/> <option value="INVALID_CIGAR"/> <option value="ADJACENT_INDEL_IN_CIGAR"/> <option value="INVALID_MATE_REF_INDEX"/> <option value="MISMATCH_MATE_REF_INDEX"/> <option value="INVALID_REFERENCE_INDEX"/> <option value="INVALID_ALIGNMENT_START"/> <option value="MISMATCH_MATE_ALIGNMENT_START"/> <option value="MATE_FIELD_MISMATCH"/> <option value="INVALID_TAG_NM"/> <option value="MISSING_TAG_NM"/> <option value="MISSING_HEADER"/> <option value="MISSING_SEQUENCE_DICTIONARY"/> <option value="MISSING_READ_GROUP"/> <option value="RECORD_OUT_OF_ORDER"/> <option value="READ_GROUP_NOT_FOUND"/> <option value="RECORD_MISSING_READ_GROUP"/> <option value="INVALID_INDEXING_BIN"/> <option value="MISSING_VERSION_NUMBER"/> <option value="INVALID_VERSION_NUMBER"/> <option value="TRUNCATED_FILE"/> <option value="MISMATCH_READ_LENGTH_AND_QUALS_LENGTH"/> <option value="EMPTY_READ"/> <option value="CIGAR_MAPS_OFF_REFERENCE"/> <option value="MISMATCH_READ_LENGTH_AND_E2_LENGTH"/> <option value="MISMATCH_READ_LENGTH_AND_U2_LENGTH"/> <option value="E2_BASE_EQUALS_PRIMARY_BASE"/> <option value="BAM_FILE_MISSING_TERMINATOR_BLOCK"/> <option value="UNRECOGNIZED_HEADER_TYPE"/> <option value="POORLY_FORMATTED_HEADER_TAG"/> <option value="HEADER_TAG_MULTIPLY_DEFINED"/> <option value="HEADER_RECORD_MISSING_REQUIRED_TAG"/> <option value="INVALID_DATE_STRING"/> <option value="TAG_VALUE_TOO_LARGE"/> <option value="INVALID_INDEX_FILE_POINTER"/> <option value="INVALID_PREDICTED_MEDIAN_INSERT_SIZE"/> <option value="DUPLICATE_READ_GROUP_ID"/> <option value="MISSING_PLATFORM_VALUE"/> <option value="INVALID_PLATFORM_VALUE"/> <option value="DUPLICATE_PROGRAM_GROUP_ID"/> <option value="MATE_NOT_FOUND"/> <option value="MATES_ARE_SAME_END"/> <option value="MISMATCH_MATE_CIGAR_STRING"/> <option value="MATE_CIGAR_STRING_INVALID_PRESENCE"/> </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** Reads a SAM/BAM dataset and report on its validity. @dataset_collections@ @description@ MODE=Mode M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the default value. Possible values: {VERBOSE, SUMMARY} IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT, INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED, INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR, INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND, INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT, INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR, ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX, INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START, MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER, MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER, READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN, MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE, MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE, MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH, E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE, POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED, HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE, INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE, DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE, DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END, MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be specified 0 or more times. MAX_OUTPUT=Integer MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can be set to 'null' to clear the default value. REFERENCE_SEQUENCE=File R=File Reference sequence file, the NM tag check will be skipped if this is missing Default value: null. IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default value: true. This option can be set to 'null' to clear the default value. Possible 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 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> </tool>