<tool id="qiime_validate_mapping_file" name="Validate mapping file" version="1.9.1">
    <description>to check for required data and format</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <version_command><![CDATA[
        validate_mapping_file.py --version
    ]]></version_command>

    <command><![CDATA[
        validate_mapping_file.py 
            -m $mapping_fp 
            -o validate_mapping_file_output
            $verbose
            -c $char_replace
            $not_barcoded
            $variable_len_barcodes
            $disable_primer_check

            #if str($added_demultiplex_field):
                -j $added_demultiplex_field
            #end if

            $suppress_html

        #if not $suppress_html:
            &&
            mkdir -p $html_report.files_path 
            &&
            cp validate_mapping_file_output/*.html $html_report.files_path  
            &&
            cp "validate_mapping_file_output/overlib.js" "$html_report.extra_files_path"
            &&
            mv $html_report.files_path/*.html $html_report
        #end if
]]>
    </command>

	<inputs>
		<param name="mapping_fp" label="Metadata mapping filepath" type="data" 
            format="tabular,csv,txt,tsv" help="(-m/--mapping_fp)"/>

        <param name="verbose" type="boolean" label="Enable printing information 
            to standard out?" truevalue="-v" falsevalue="" checked="False" 
            help="(-v/--verbose)" />

		<param name="char_replace" type="text" value="_" label="Default character 
            used to replace invalid characters found in the mapping file"  
            help="Must be a valid character (alphanumeric, period, or underscore). 
            (-c/--char_replace)"/>

		<param name="not_barcoded" type="boolean" label="Are barcodes present?" 
            truevalue="" falsevalue="--not_barcoded" checked="True" 
            help="BarcodeSequence header is still required in mapping file 
            (-b/--not_barcoded)"/>

        <param name="variable_len_barcodes" type="boolean" label="Are barcodes with
            variable length?" truevalue="" falsevalue="--variable_len_barcodes" 
            checked="True" help="(-B/--variable_len_barcodes)"/>

        <param name="disable_primer_check" type="boolean" label="Disable checks 
            for primers?" truevalue="-disable_primer_check" falsevalue="" 
            checked="False" help="LinkerPrimerSequence header is still required 
            in mapping file (-p/--disable_primer_check)"/>

		<param name="added_demultiplex_field" type="text" label="Field
            to use in the mapping file as additional demultiplexing (optional)"
            help="It can be used with or without barcodes.  All combinations of 
            barcodes/primers and these fields must be unique. The fields must contain 
            values that can be parsed from the fasta labels such as 'plate=R_2008_12_09'.  
            In this case, 'plate' would be the column header and 'R_2008_12_09'
             would be the field data (minus quotes) in the mapping file.  
             To use the run prefix from the fasta label, such as 'FLP3FBN01ELBSX',
            where 'FLP3FBN01' is generated from the run ID, use 'run_prefix' and 
            set the run prefix to be used as the data under the column header 
            'run_prefix' (-j/--added_demultiplex_field)" optional="True"/>

        <param name="suppress_html" type="boolean" label="Disable html file 
            generation?" truevalue="-s" falsevalue="" checked="False" 
            help="It can be useful for extremely large mapping files 
            (-s/--suppress_html)"/>
    </inputs>

	<outputs>
        <data name="html_report" format="html" 
            label="${tool.name} on ${on_string}: html report">
            <filter>suppress_html is False</filter>
        </data>
		<data name="log" format="txt"
            from_work_dir="validate_mapping_file_output/*.log"
            label="${tool.name} on ${on_string}: log"/>
        <data format="tabular" name="mapping_fp_corrected" 
            from_work_dir="validate_mapping_file_output/*corrected.txt"
            label="${tool.name} on ${on_string}: corrected map" />
    </outputs>

    <tests>
        <test>
            <param name="mapping_fp" value="map.tsv"/>
            <param name="verbose" value="" />
            <param name="char_replace" value="_" />
            <param name="not_barcoded" value="" />
            <param name="variable_len_barcodes" value="" />
            <param name="disable_primer_check" value="" />
            <param name="suppress_html" value="" />

            <output name="log" file="validate_mapping_file_log.txt"/>
            <output name="mapping_fp_corrected" 
                file="validate_mapping_file_corrected_map.tabular"/>
        </test>
    </tests>

    <help><![CDATA[
**What it does?**

This tool checks user’s metadata mapping file for required data, valid format

Specifically, it checks that:

    - The BarcodeSequence, LinkerPrimerSequences, and ReversePrimer fields have valid IUPAC DNA characters, and BarcodeSequence characters are non-degenerate (error)
    - The SampleID, BarcodeSequence, LinkerPrimerSequence, and Description headers are present. (error)
    - There are not duplicate header fields (error)
    - There are not duplicate barcodes (error)
    - Barcodes are of the same length.  Suppressed when variable_len_barcode flag is passed (warning)
    - The headers do not contain invalid characters (alphanumeric and underscore only) (warning)
    - The data fields do not contain invalid characters (alphanumeric, underscore, space, and +-%./:,; characters) (warning)
    - SampleID fields are MIENS compliant (only alphanumeric and . characters). (warning)
    - There are no duplicates when the primer and variable length barcodes are appended (error)
    - There are no duplicates when barcodes and added demultiplex fields (-j option) are combined (error)
    - Data fields are not found beyond the Description column (warning)

More information about this tool is available on 
`QIIME documentation <http://qiime.org/scripts/validate_mapping_file.html>`_.
    ]]>
    </help>

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

</tool>