<tool id="csvtk_correlation" name="csvtk-correlation" version="@VERSION@+@GALAXY_VERSION@">
    <description> calculate pearson correlation</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_cmd" />
    <command detect_errors="exit_code"><![CDATA[

###################
## Start Command ##
###################

csvtk corr --num-cpus "\${GALAXY_SLOTS:-1}"

    ## Add additional flags as specified ##
    #######################################
    $global_param.illegal_rows
    $global_param.empty_rows
    $global_param.header
    $global_param.lazy_quotes

    ## Set Tabular input/output flag if input is tabular ##
    #######################################################
    #if $in_1.is_of_type("tabular"):
        -t -T
    #end if

    ## Specify fields ##
    ####################
    -f '$in_text'

    ## Set Input ##
    ###############
    '$in_1'

    ## other ##
    ###########
    $ignore_nan
    $log_values
    $passthrough

    ## To output ##
    ###############
    &> corr

    ]]></command>
    <inputs>
        <expand macro="singular_input" />
        <param name="in_text" type="text" argument="-f"
            label="Specify *two* column names"
            help="Input the exact spelling of the two input column names wanted with a comma (,) separating them. Ex. 'Length,GC Content'">
            <expand macro="text_sanitizer" />
        </param>
        <param name="ignore_nan" type="boolean" checked="false" argument="-i"
            truevalue="-i"
            falsevalue=""
            label="Ignore non-numeric values in columns"
            help="Needed to be set to yes to avoid returning NaN if there is a non-numeric value"
        />
        <param name="log_values" type="boolean" checked="false" argument="-L"
            truevalue="-L"
            falsevalue=""
            label="Log10 transformed Data"
            help="Calcute correlations on Log10 transformed data"
        />
        <param name="passthrough" type="boolean" checked="false" argument="-x"
            truevalue="-x"
            falsevalue=""
            label="passthrough mode (forward input to output)"
        />
        <expand macro="global_parameters" />
    </inputs>
    <outputs>
        <data format_source="in_1" name="corr" from_work_dir="corr" label="${in_1.name} correlation of ${in_text}" />
    </outputs>
    <tests>
        <test>
            <param name="in_1" value="XY_converted.csv" />
            <param name="in_text" value="X,Y" />
            <output name="corr" value="corr_1.csv" />
        </test>
        <test>
            <param name="in_1" value="XY_converted.tsv" />
            <param name="in_text" value="X,Y" />
            <param name="ignore_nan" value="true" />
            <param name="log_values" value="true" />
            <param name="passthrough" value="true" />
            <output name="corr" value="corr_2.tsv" />
        </test>
    </tests>
    <help><![CDATA[
    
Csvtk - Correlation Help
------------------------

Info
####

Csvtk Correlation calculates the pearson correlation between two columns specified by the column header 

.. class:: warningmark

    Single quotes are not allowed in text inputs!

@HELP_INPUT_DATA@


Usage
#####

To run csvtk-correlation, all you need is a valid (as defined above) CSV or TSV file with two numeric columns that you want to
find the pearson correlation between. If the input data is Log10 transformed, remember to set the "Log10 transformed Data" 
slider to "Yes"

Output will be a singular line with the input column names, and the pearson correlation (integer between -1 to 1).


**Example Correlation Input**

Input table:

+-------+--------+
| Group | Length | 
+=======+========+
| 1     | 1500   |
+-------+--------+
| 2     | 1000   |
+-------+--------+
| 1     | 1500   |
+-------+--------+
| 3     | 2000   |
+-------+--------+

Our input for this would require us to specify our column input (-f) as "Group,Length" to allow the program to run

Our output would then look as such:

+-------+--------+--------+
| Group | Length | 0.9999 |
+-------+--------+--------+

--------


@HELP_COLUMNS@


@HELP_END_STATEMENT@


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