<tool id="secimtools_threshold_based_flags" name="Threshold Based Flags" version="@WRAPPER_VERSION@">
    <description>to flag features based on a user-specified threshold.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command><![CDATA[
threshold_based_flags.py
--input $input
--design $design
--ID $uniqID
--output $output
--group $group

#if $cutoff:
--cutoff $cutoff
#end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
        <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
        <param name="group" type="text" size="30" label="Group/Treatment" help="Name of the column in your Design File that contains group classifications.  The resulting indicator flags will generated for these group categories." />
        <param name="cutoff" type="integer" optional="true" size="6" value="30000" label="Cutoff" help="Cutoff to use for which values to flag. Defaults = 30,000."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input"   value="ST000006_data.tsv"/>
            <param name="design"  value="ST000006_design.tsv"/>
            <param name="uniqID"  value="Retention_Index" />
            <param name="group"   value="White_wine_type_and_source" />
            <param name="cutoff"  value="3000" />
            <output name="output" file="ST000006_threshold_based_flags_output.tsv" />
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

This tool flags a feature in a given group with a binary indicator if, for half (or more) of the samples within the group, the feature value is below a user specified threshold or is missing.
The default threshold value of 30,000 is primarily useful for peak intensities from mass spectroscopy data and should be evaluated carefully for other types of values (e.g. for peak height).

--------------------------------------------------------------------------------


**Input**

    - Two input datasets are required.

@WIDE@

**NOTE:** The sample IDs must match the sample IDs in the Design File (below).
Extra columns will automatically be ignored.

@METADATA@

@UNIQID@

@GROUP@

**Cutoff Value**

    - Cutoff to use for which values to flag. Default = 30,000.

--------------------------------------------------------------------------------

**Output**

This tool outputs a TSV file containing indicator flags for each group, where the number of indicator flags is determined by the number of groups.

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