<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>normalize fasta datasets</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
    @java_options@

    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
    #import re
    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
    ln -sf '$inputFile' '$escaped_element_identifier'.fa &&
    
    picard NormalizeFasta

    --INPUT '$escaped_element_identifier'.fa
    --OUTPUT '${outFile}'
    --LINE_LENGTH '${line_length}'
    --TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE '${truncate_sequence_names_at_whitespaces}'

    --QUIET true
    --VERBOSITY ERROR

  ]]></command>
    <inputs>
        <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset"/>
        <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/>
        <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/>
    </inputs>
    <outputs>
        <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/>
    </outputs>
    <tests>
        <test>
            <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/>
            <param name="line_length" value="40"/>
            <param name="truncate_sequence_names_at_whitespaces" value="False"/>
            <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/>
        </test>
    </tests>
    <help>

**Purpose**

Takes any dataset that conforms to the fasta format and normalizes it so that all lines of sequence except the last line per named sequence are of the same length.

@dataset_collections@

@description@

  LINE_LENGTH=Integer           The line length to be used for the output fasta file.  Default value: 100.

  TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean
                                Truncate sequence names at first whitespace.  Default value: false. Possible values: {true, false}

@more_info@

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