<tool name="ReorderSam" id="picard_ReorderSam" version="@TOOL_VERSION@.0">
  <description>reorder reads to match ordering in reference sequences</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    #set $picard_dict = "localref.dict"
    #set $ref_fasta = "localref.fa"     ## This is done because picards "likes" .fa extension

    ln -s "${reference_source.ref_file}" "${ref_fasta}" &&

    #if str( $reference_source.reference_source_selector ) == "history":

      picard CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"
      QUIET=true
      VERBOSITY=ERROR

      &&

    #else:

      #set $ref_fasta = str( $reference_source.ref_file.fields.path )

    #end if

    picard
    ReorderSam
      INPUT='$escaped_element_identifier'
      OUTPUT="${outFile}"
      REFERENCE="${ref_fasta}"
      ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"
      ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"

      VALIDATION_STRINGENCY="${validation_stringency}"
      QUIET=true
      VERBOSITY=ERROR

  ]]></command>

  <inputs>

     <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 format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
    <param name="allow_incomplete_dict_concordance" type="boolean" label="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs" help="ALLOW_INCOMPLETE_DICT_CONCORDANCE; By default, this tool requires a corresponding contig in the new reference for each read contig; default=False"/>
    <param name="allow_contig_length_discordance" type="boolean" label="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length" help="ALLOW_CONTIG_LENGTH_DISCORDANCE; HIGHLY DANGEROUS! Only use if you know what you are doing; default=False"/>
    <expand macro="VS" />

  </inputs>
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: Reordered BAM"/>
  </outputs>
  <tests>
    <test>
      <param name="reference_source_selector" value="history" />
      <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />
      <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>
      <param name="allow_incomplete_dict_concordance" value="false"/>
      <param name="allow_contig_length_discordance" value="false"/>
      <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="4"/>
    </test>
  </tests>


  <help>

.. class:: infomark

**Purpose**

ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs.  Reads mapped to contigs absent in the new reference are dropped.

@dataset_collections@

----

.. class:: warningmark

Not to be confused with **SortSam**.

@description@

  ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean
  S=Boolean                     If true, then allows only a partial overlap of the BAM contigs with the new reference
                                sequence contigs.  By default, this tool requires a corresponding contig in the new
                                reference for each read contig  Default value: false. Possible values: {true, false}

  ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean
  U=Boolean                     If true, then permits mapping from a read contig to a new reference contig with the same
                                name but a different length.  Highly dangerous, only use if you know what you are doing.
                                Default value: false.  Possible values: {true, false}

@more_info@
  </help>
</tool>