<tool id="straindesign_analyzing_model" name="StrainDesign analyzing-model" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
    <description>Produce a pareto plot for a biological model</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command detect_errors="exit_code"><![CDATA[
        ## Run cmdline
        python -m straindesign analyzing-model
            @CMD_INPUT_MODEL@
            @CMD_INPUT_MEDIUM@
            @CMD_BIOMASS_RXN_ID@
            @CMD_TARGET_RXN_ID@
            @CMD_INPUT_PATHWAY@
            #if str('$substrate_cond.substrate_param') == 'yes'
                --substrate-rxn-id '$substrate_cond.substrate_rxn_id'
            #end if
            --output-pareto-png '$output_png'
    ]]></command>
    <expand macro="env_variables"/>
    <inputs>
        <expand macro="input_model_sbml"/>
        <expand macro="input_medium_tsv"/>
        <expand macro="input_biomass_rxn_id"/>
        <expand macro="input_target_rxn_id"/>
        <expand macro="input_pathway_sbml"/>
        <conditional name="substrate_cond">
            <param name="substrate_param" type="select" label="Provide a substrate reaction" help="Choose yourself a carbon source or it will be detected automatically">
                <option value="yes">yes</option>
                <option value="no" selected="true">No</option>
            </param>
            <when value="yes">
                <expand macro="input_substrate_rxn_id"/>
            </when>
            <when value="no"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_png" format="png" label="${tool.name}" />
    </outputs>
    <tests>
        <test>
            <!--  test 1  -->
            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
            <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
            <param name="target_rxn_id" value="EX_tyrp_e" />
            <output name="output_png" ftype="png">
                <assert_contents>
                    <has_size value="30000" delta="10000"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <!--  test 2  -->
            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
            <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
            <param name="target_rxn_id" value="EX_tyrp_e" />
            <param name="substrate_rxn_id" value="EX_glc__D_e" />
            <output name="output_png" ftype="png">
                <assert_contents>
                    <has_size value="30000" delta="10000"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <!--  test 3  -->
            <param name="model" ftype="sbml" value="iAF1260.xml.gz"/>
            <param name="pathway" ftype="sbml" value="butanol.xml" />
            <param name="medium" ftype="tabular" value="butanol.tsv" />
            <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
            <param name="substrate_rxn_id" value="EX_glc__D_e" />
            <param name="target_rxn_id" value="EX_1btol_e" />
            <output name="output_png" ftype="png">
                <assert_contents>
                    <has_size value="30000" delta="10000"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_TITLE@

This tool produces a phenotypic-phase-plane plot given these datas:
* model
* reaction producing a target
* biomass reaction
These informations are optionals and will be adapted to your needs:
* an heterologous pathway
* a carbon substrate
* media composition

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