<tool id="retip_apply" name="Retip prediction" version="@TOOL_VERSION@+galaxy3">
    <description>is retention time predictor for Metabolomics</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>

    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
            #if $input_smiles.is_of_type('tabular')
               /run.sh spell_tsv.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --name '$name_col' --smiles '$smiles_col' --out 'output_file' --bad 'bad_file'
            #else
               /run.sh spell_h5.R --desc '$descr_train' --model '$model_h5' --inp '$input_smiles' --ids '$ids' --ods '$ods' --name '$name_col' --smiles '$smiles_col' --out 'output_file' --bad 'bad_file'
            #end if
      ]]>
    </command>
    <inputs>
        <param name="descr_train" label="Select Descriptors.h5 Dataset" type="data" format="h5" optional="false"/>
        <param name="model_h5" label="Select Model.h5 Dataset" type="data" format="h5" optional="false"/>
        <param format="tabular,h5" name="input_smiles" type="data" label="Select Input Smiles tsv or h5 Dataset"
               optional="false"/>
        <param name="smiles_col" type="text" label="Name of input column with SMILES" optional="true"
               value="qsar_smiles"/>
        <param name="name_col" type="text" label="Name of input column with some unique identifier" optional="true"
               value="recetox_cid"/>
        <param name="ids" type="text" label="Input H5 dataset" optional="true" value="/annotations"/>
        <param name="ods" type="text" label="Output H5 dataset" optional="true" value="/annotations"/>
    </inputs>
    <outputs>
        <data format_source="input_smiles" name="output_good" label="Predicted RT" from_work_dir="output_file"/>
        <data format_source="input_smiles" name="output_bad" label="Failed RT prediction" from_work_dir="bad_file"/>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="descr_train" value="descriptors.h5"/>
            <param name="model_h5" value="model.h5"/>
            <param name="input_smiles" value="pubchem-99.tsv"/>
            <output name="output_good" file="pubchem-good.tsv" ftype="tabular"/>
            <output name="output_bad" file="pubchem-bad.tsv" ftype="tabular"/>
        </test>
        <test expect_num_outputs="2">
            <param name="descr_train" value="descriptors.h5"/>
            <param name="model_h5" value="model.h5"/>
            <param name="input_smiles" value="input.h5"/>
            <param name="ids" value="/compounds/table"/>
            <param name="ods" value="/compounds"/>
            <output name="output_good" file="good.h5" ftype="h5" compare="sim_size" delta="50"/>
            <output name="output_bad" file="bad.h5" ftype="h5" compare="sim_size" delta="50"/>
        </test>
    </tests>
    <help>
        <![CDATA[
        .. class:: infomark

        This tool is used for **Retention Time Prediction** on a whole database.

        @HELP@
        ]]>
    </help>
    <expand macro="citations"/>
</tool>