<tool id="revoluzer_crex" name="CREx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>reconstruct pairwise gene order rearrangement</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <version_command>crex --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        crex 
            -f '$f'
            $linear
            $method_cond.method_select
            #if $method_cond.method_select == ""
                $noalt
                --wI $wI
                --wiT $wiT
                --wiT $wTDRL
            #else if $method_cond.method_select == "--crex1"
                $prinobp
            #end if
            > '$out'
    ]]></command>
    <inputs>
        <param argument="-f" type="data" format="fasta" label="Gene orders"/>
        <param argument="--linear" type="boolean" truevalue="--linear" falsevalue="" checked="false" label="Genomes are linear"/>
        <conditional name="method_cond">
            <param name="method_select" type="select" label="method">
                <option value="">CREx2</option>
                <option value="--crex1" selected="true">CREx1</option>
                <option value="--bp">compute with breakpoint scenario [ZhaoBourque07]</option>
            </param>
            <when value="">
                <param argument="--wI" type="float" min="0" value="1" label="Weight of an inversion"/>
                <param argument="--wiT" type="float" min="0" value="1" label="Weight of an inverse transposition"/>
                <param argument="--wTDRL" type="float" min="0" value="1" label="Weight of a TDRL"/>
                <param argument="--noalt" type="boolean" truevalue="" falsevalue="--noalt" checked="true" label="Compute alternatives for T+iT"/>
            </when>
            <when value="--crex1">
                <param argument="--prinobp" type="boolean" truevalue="" falsevalue="--prinobp" checked="true" label="Compute breakpoint scenario for prime nodes"/>
            </when>
            <when value="--bp"></when>
        </conditional>
    </inputs>
    <outputs>
        <data name="out" format="tabular">
            <actions>
                <action name="column_names" type="metadata" default="Source gene order,Target Gene order,Rearrangement,Breakpoints" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="f" value="test.fas"/>
            <param name="linear" value="true"/>
            <output name="out">
                <metadata name="column_names" value="Source gene order,Target Gene order,Rearrangement,Breakpoints" />
                <assert_contents>
                    <has_n_lines n="7"/>
                    <has_n_columns n="4"/>
                    <has_text text="I(B C )"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

Compute rearrangement scenarios on pairs of gene orders (with equal duplication free gene content).

Usage
.....

**Input**

@INPUT_FORMAT@

**Output**

Rearrangements in the 3rd column of the outbut table are listed as follows:

- I(X): the genes listed in X are inverted
- T(X ,Y ,): The order of the gene sets X and Y is transposed
- iT(X, Y, ): Same as transposition, but one gene of the sets is also inverted
- TDRL(X, Y): A tandem duplication random loss where the genes in X are kept in the 1st copy and the genes in Y an the last

    ]]></help>
    <citations>
        <citation type="doi">10.1109/TCBB.2018.2831661</citation>
        <citation type="doi">10.1093/bioinformatics/btm468</citation>
        <citation type="doi">10.1007/978-3-540-74960-8_12</citation>
    </citations>
</tool>