<tool id="straindesign_reduce_model" name="StrainDesign reduce-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
    <description>Delete gene in a biological model</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command detect_errors="exit_code"><![CDATA[
        python -m straindesign reduce-model
            @CMD_INPUT_MODEL@
            #if str($sd_strategy.sd_cond) == 'yes'
                --input-straindesign-file '$sd_strategy.sd_tsv'
                --parameter-strategy-str '$sd_strategy.sd_strategy_str'
            #end if
            --output-file-sbml '$output_sbml'
            #if str($input_gene_str) != ''
                --input-gene-str #echo $input_gene_str
            #end if
    ]]></command>
    <expand macro="env_variables"/>
    <inputs>
        <expand macro="input_model_sbml"/>
        <conditional name="sd_strategy">
            <param name="sd_cond" type="select" label="Fill with the output of StrainDesign simulate-deletion">
                <option value="no" selected="True">no</option>
                <option value="yes" >yes</option>
            </param>
            <when value="yes">
                <param name="sd_tsv" type="data" format="tabular" label="StrainDesign simulate-deletion output" help="TSV input file"/>
                <param name="sd_strategy_str" type="select" label="Strategy" help="Choose which genes will be deleted automatically">
                    <option value="yield-max" selected="True">Yield Max</option>
                    <option value="gene-max">Gene Max</option>
                    <option value="gene-min"> Gene Min</option>
                </param>
            </when>
            <when value="no"/>
        </conditional>
        <param name="input_gene_str" type="text" value="" label="Gene IDs" help="Multiple genes are separated by space">
            <validator type="regex" message="No special characters allowed">^(?:[ \w.-])*$</validator>
        </param>
    </inputs>
    <outputs>
        <data name="output_sbml" format="sbml" label="${tool.name}" />
    </outputs>
    <tests>
        <test>
            <!--  test 1  -->
            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
            <param name="input_gene_str" value="b4208 b4208 b3919"/>
            <output name="output_sbml" ftype="sbml">
                <assert_contents>
                    <is_valid_xml/>
                    <not_has_text text="b4208"/>
                    <not_has_text text="b3919"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <!--  test 2  -->
            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
            <param name="sd_cond" value="yes"/>
            <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
            <output name="output_sbml" ftype="sbml">
                <assert_contents>
                    <is_valid_xml/>
                    <not_has_text text="b3919"/>
                    <not_has_text text="b0529"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <!--  test 3  -->
            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
            <param name="sd_cond" value="yes"/>
            <param name="sd_tsv" ftype="tabular" value="simulate_deletion.butanol.iAF1260.tsv"/>
            <param name="input_gene_str" value="b4208 b4208 b3919"/>
            <output name="output_sbml" ftype="sbml">
                <assert_contents>
                    <is_valid_xml/>
                    <not_has_text text="b4208"/>
                    <not_has_text text="b3919"/>
                    <not_has_text text="b0529"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_TITLE@

This tool deletes some genes provided either from **simulate-deletion¨** or provided by their ids, in a biological model (SBML format).
If you provide a TSV file coming from the **simulate-deletion** commands either the file is cleanned by hand and contains one line or the program tries to identify which genes will be deleted by applying the suited strategy:
* yield-max: the combination of genes with the maximum amount of yiel is taken
* gene-max: the combination of genes with the maximum number of genes is taken
* gene-min: the combination of genes with the minimum number of genes is taken

@HELP_LINK@
    ]]></help>
    <expand macro="creator"/>
    <expand macro="citation"/>
</tool>