<tool id="picrust2_shuffle_predictions" name="PICRUSt2 Generation of shuffled predictions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>for a specified number of replicates</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tool"/>
    <expand macro="requirements"/>
    <version_command>shuffle_predictions.py -v</version_command>
    <command detect_errors="exit_code"><![CDATA[
ln -s '$input' predicted.tsv &&
shuffle_predictions.py
    --input predicted.tsv
    --outdir predicted_shuffled
    --rep $rep
#if str($seed) != ''
    --seed $seed
#end if
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="tabular" label="Input prediction table"/>
        <param argument="--rep" type="integer" min="1" value="1" label="Number of shuffled replicates to create"/>
        <param argument="--seed" type="integer" optional="true" label="Random seed" help="Set this for reproducible shufflings"/>
    </inputs>
    <outputs>
        <collection name="predicted_shuffled" type="list">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="predicted_shuffled/" format="tabular"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="EC_predicted.tsv.gz"/>
            <param name="rep" value="5"/>
            <param name="seed" value="131"/>
            <output_collection name="predicted_shuffled" type="list" count="5">
                <element name="predicted_shuf1.tsv" ftype="tabular">
                    <assert_contents>
                        <has_text text="8db33d54e5184b0f448ae140f793368a"/>
                        <has_n_lines n="38"/>
                    </assert_contents>
                </element>
                <element name="predicted_shuf2.tsv" ftype="tabular">
                    <assert_contents>
                        <has_text text="763af2e6cfd1d573893fa6d28aafc4b5"/>
                        <has_n_lines n="38"/>
                    </assert_contents>
                </element>
                <element name="predicted_shuf3.tsv" ftype="tabular">
                    <assert_contents>
                        <has_text text="f5b23f626e3f2d2d1213f83c6de3e385"/>
                        <has_n_lines n="38"/>
                    </assert_contents>
                </element>
                <element name="predicted_shuf4.tsv" ftype="tabular">
                    <assert_contents>
                        <has_text text="ff33233ffebbe6e3720af8bba7e89f08"/>
                        <has_n_lines n="38"/>
                    </assert_contents>
                </element>
                <element name="predicted_shuf5.tsv" ftype="tabular">
                    <assert_contents>
                        <has_text text="691eeed271e420c8e7a91d5ea0cf5431"/>
                        <has_n_lines n="38"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Generating shuffled predictions
===============================
Shuffles sequence ids of prediction table for a specified number of replicates.

Note
====
This means that the prediction table is not totally scrambled across all colunmns: each predicted genome is still the same, but the sequence ids (e.g. the ASV id) linked with each predicted genome is randomized.

Input
=====
Prediction table

Output
======
Predicted shuffled table

    ]]></help>
    <citations>
        <citation type="doi">10.1038/s41587-020-0548-6</citation>
    </citations>
</tool>