<tool id="secimtools_magnitude_difference_flags" name="Magnitude Difference Flags" version="@WRAPPER_VERSION@">
    <description>- Count the number of digits before the decimal place.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
magnitude_difference_flags.py
--input $input
--design $design
--ID $uniqID
--flags $flags
--figure $figure
--counts "counts"
--html $html
--htmlPath "$html.files_path"

#if $nozero:
    --noZero
#end if
#if $group:
    --group $group
#end if
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If file is not tab separated see TIP below."/>
        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique identifiers.."/>
        <param name="nozero" type="select" size="30" display="radio" value="yes" label="Remove zeros before processing" help="If not removed, zeros may skew the results.">
            <option value="yes">Remove zeros</option>
            <option value="no">Do not remove zeros</option>
        </param>
        <param name="group" size="30" type="text" label="Group/Treatment [Optional]" help="Name of the column in your Design File that contains group classifications." />
    </inputs>
    <outputs>
        <data format="pdf" name="figure"  label="${tool.name} on ${on_string}: Figure" />
        <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags" />
        <data format="html" name="html" label="${tool.name} on ${on_string}: Counts" />
    </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="nonzero" value="yes" />
            <output name="figure" file="ST000006_magnitude_difference_flags_figure.pdf" compare="sim_size" delta="10000"/>
            <output name="flags"  file="ST000006_magnitude_difference_flags_flags.tsv" />
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

This tool counts the number of digits before the decimal place for each feature in each sample.
The tool identifies features with different orders of magnitude across different samples in a given group and produces corresponding indicator flags.
Unusual samples are identified by finding systematically low or high feature values for that particular sample.

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

**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@

**Remove zeros before processing**

  - If zeros are not removed before processing, they may skew the results.

@GROUP_OPTIONAL@

**NOTE:** Groups with one element will be excluded from the test.

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

**Output**

The tool outputs a variable number of files (from 2 to n+1) depending on the number of groups (n).

(1) TSV file containing a 0/1 indicator flag where “1” is used to flag features where the difference in the digit counts is greater than 2.

(2) TSV file containing the digit counts for all samples or for the samples within groups,  depending on whether the Group/Treatment [Optional] parameter was provided.

(3) A PDF file of the distribution of digit counts within each group of samples.

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