<tool id="ct_check_labels" name="Cell types - check labels" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>filters non-alphanumeric characters from labels</description>
    <macros>
        <import>ct_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[

        check_labels.R --input-file "${input_file}"  --condensed "${condensed}" --attribute-type-col-num "${attribute_type_col_num}" --variable-col-num "${variable_col_num}" --avoid-lowercase "${avoid_lowercase}" --output-path "${output_path}"

        #if $label_field
        --label-field "${label_field}"
        #end if

        ]]></command>
        <inputs>
            
            <param type="data" name="input_file" label="Input File" multiple="true" format="txt" help="Input metadta file" />
            <param type="text" name="label_field" label="Label Field" optional="true" help="Name of label field in metadata file">
                <expand macro="sanitize_strings" />
            </param>
            <param type="boolean" name="condensed" checked="false" label="Condensed Metadata File" help="Are the supplied metadata files of condensed format?" /> 
            <param type="integer" name="attribute_type_col_num" value='5' label="Number of Attribute Type Column" help="Number of the attribute type field in condensed metadata file. Default: 5" />
            <param type="integer" name="variable_col_num" value='6' label="Number of Label Column" help="Number of the label field in condensed metadata file. Default: 6" />
            <param type="boolean" name="avoid_lowercase" checked="false" label="Avoid Lowercaase" help="Should setting the labels to lowercase be skipped? Default: False" /> 

        </inputs>
        <outputs>
            <data name="output_path" format="txt" />
        </outputs>
        <tests>
        <test>
            <param name="input_file" value="SDRFs/E-ENAD-27.condensed-sdrf.tsv" />
            <param name="label_field" value="inferred cell type" />
            <param name="condensed" value="TRUE" />
            <output name="output_path" file="checked_SDRF.tsv" compare="sim_size" />
        </test>
    </tests>
        <help><![CDATA[
    @HELP@
    
    @VERSION_HISTORY@
    ]]></help>
    <expand macro="citations" />
</tool>