<tool id="rcx-tk" name="rcx-tk" version="0.1.0+galaxy0" python_template_version="3.5" profile="23.05">
    <edam_topics>
        <edam_topic>topic_3172</edam_topic>
        <edam_topic>topic_0091</edam_topic>
        <edam_topic>topic_3520</edam_topic>       
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0336</edam_operation>
        <edam_operation>operation_3695</edam_operation> 
    </edam_operations>
    <requirements>
        <requirement type="package" version="0.1.0">rcx-tk</requirement>
    </requirements>
    <creator>
        <person
                givenName="Zargham"
                familyName="Ahmad"
                url="https://github.com/zargham-ahmad"
                identifier="0000-0000-0000-0000"/>
        <person
                givenName="Kristina"
                familyName="Gomoryova"
                url="https://github.com/KristinaGomoryova"
                identifier="0000-0003-4407-3917" />
        <person
                givenName="Helge"
                familyName="Hecht"
                url="https://github.com/hechth"
                identifier="0000-0001-6744-996X" />
        <organization 
                url="https://www.recetox.muni.cz/"
                email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
                name="RECETOX MUNI" />  
    </creator>
    <command><![CDATA[
    #if $input_file.ext == "tabular"
        #set $input_file_new = 'input.tsv'
    #else
        #set $input_file_new = 'input.' + str($input_file.ext)
    #end if
       cp ${input_file} ${input_file_new} &&
       python3 -m rcx_tk --method ${method} ${input_file_new} 'output.tsv' 
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="csv,tabular,tsv,xls,xlsx,txt" label="Input data" help="Input data"/>
        <param name="method" type="select" label="Method" help="Which data is processed: metadata or alkane file.">
            <option value="metadata" selected="true">metadata</option>
            <option value="alkanes">alkanes</option>
        </param>
    </inputs>
    <outputs>
        <data name="output_file" format="tabular" from_work_dir = "output.tsv" label="Processed data"/>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="input_metadata.tabular"/>
            <param name="method" value="metadata"/>
            <output name="output_file" file="output_metadata.tsv"/>
        </test>
         <test>
            <param name="input_file" value="input_alkanes.txt"/>
            <param name="method" value="alkanes"/>
            <output name="output_file" file="output_alkanes.tsv"/>
        </test>
    </tests>
    <help><![CDATA[
    rcx-tk is a tool to process a metadata and/or alkane files. The main steps are columns rearrangement, validation of the file names, and derivation of new columns, such as sampleName, sequenceIdentifier, sampleIdentifier and localOrder. 

    On the input, a metadata or alkane file in any tabular format is expected. On the output, a tsv file is provided.
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.4471245</citation>
    </citations>
</tool>