<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[

    ##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}"
    VALIDATE_INDEX="${validate_index}"
    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">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**

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>
  <expand macro="citations" />
</tool>