<tool id="secimtools_ttest_perm" name="Group Comparison by Permutation" version="@WRAPPER_VERSION@">
    <description>on features.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
ttest_perm.py
--input $input
--design $design
--uniqueID $uniqueID
--group $group
--reps $reps
--summaries $summaries
--flags $flags
--volcano $volcano
    </command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/>
        <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/>
        <param name="uniqueID" type="text" size="30" value="" label="Unique Feature ID"  help="Name of the column in your Wide Dataset that has unique Feature IDs."/>
        <param name="group" type="text" size="30"             label="Group/Treatment"    help="Name of the column in your Design File that contains group classifications."/>
        <param name="reps"  type="text" size="30"    value="" label ="Iteration Number." help="Enter the number of iterations you want to carry out."/>
    </inputs>
    <outputs>
        <data format="tabular" name="summaries" label="${tool.name} on ${on_string}: Summaries that include p-values and mean differences."/>
        <data format="tabular" name="flags" label="${tool.name} on ${on_string}: Flags that include 0.01,  0.05 and  0.10 significance levels for the differences. "/>
        <data format="pdf" name="volcano" label="${tool.name} on ${on_string}: Volcano plots for the differences."/>
    </outputs>
    <tests>
        <test>
            <param name="input"    value="fly_test_sbys.tsv"/>
            <param name="design"   value="fly_test_design.tsv"/>
            <param name="uniqueID" value="rowID" />
            <param name="group"    value="mating_source" />
            <param name="reps"     value="1000" />
            <output name="summaries" file="fly_ttest_permuted_summary.tsv" />
            <output name="flags"     file="fly_ttest_permuted_flags.tsv" />
            <output name="volcano"   file="fly_ttest_permuted_volcano.pdf" compare="sim_size" delta="10000"/>
        </test>
    </tests>
    <help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

The tool performs a permuted two-sided t-test for multiple (two or more) groups of independent sample (unpaired or independent t-test).
The user selects the number of iterations to perform.

In an unpaired t-test the samples within and between groups are independent.  The p-value is calculated by permutation of the data.
The permutation test is performed for all pairs of conditions specified using the Group/Treatment field and for the number of specified iterations.
If there are three treatment conditions (Control, Time1 and Time2) then t-tests will be performed for: (i) Control vs Time1, (ii) Control vs Time2, and (iii) Time1 vs Time2.
Note that this will give slightly different results than the contrast in an ANOVA because the ANOVA uses all groups to estimate the error.

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

**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/Treatment**

        - List with the name of the column the Design File that contains group classifications.

** Reps**
 
        - Number of iterations (permutations) to carry out

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

**Output**

The tool outputs 3 files:

(1) a TSV file with the results table containing p-values for each test and the corresponding differences between the means for comparisons between the groups.
(2) a TSV file with an indicator flag = 1 if the difference between the groups is statistically significant using provided α levels.
(3) a PDF file with volcano plots visual inspection of the differences between group means and p-values. The red dashed line in volcano plot(s) corresponds to a p-value = 0.01 cutoff (2 on the negative log base 10 scale).

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