<tool id="straindesign_simulate_deletion" name="StrainDesign simulate-deletion" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" license="@LICENCE@">
    <description>Search genes to delete 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 simulate-deletion
            @CMD_INPUT_MODEL@
            @CMD_INPUT_PATHWAY@
            @CMD_INPUT_MEDIUM@
            @CMD_BIOMASS_RXN_ID@
            @CMD_TARGET_RXN_ID@
            --strategy '$input_strategy.strategy'
            #if str($input_strategy.strategy) == 'ko':
                --substrate-rxn-id '$input_strategy.substrate_rxn_id'
                #if $input_strategy.annotate:
                    --email '$__user_email__'
                #end if
            #end if
            #if str($max_time_cond.max_time_param) == 'yes':
                --max-time '$max_time_cond.max_time'
            #end if
            --max-knockouts '$max_knockouts'
            --output-file-tsv '$output_tsv'
    ]]></command>
    <expand macro="env_variables"/>
    <inputs>
        <expand macro="input_model_sbml"/>
        <expand macro="input_pathway_sbml"/>
        <expand macro="input_medium_tsv"/>
        <expand macro="input_biomass_rxn_id"/>
        <expand macro="input_target_rxn_id"/>
        <conditional name="input_strategy">
            <param name="strategy" type="select" label="Strategy" help="Genes or Reactions to delete">
                <option value="ko" selected="True">Gene knockouts</option>
                <option value="ou" >Reaction knockouts</option>
            </param>
            <when value="ko">
                <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters">
                    <validator type="empty_field" message="Substrate reaction ID is required"/>
                    <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
                </param>
                <param name="annotate" type="boolean" label="Annotate the genes" checked="false" help="Please agree to use your email for query the NCBI website to annotate the genes"/>
            </when>
            <when value="ou">
            </when>
        </conditional>
        <param name="max_knockouts" type="integer" min="1" max="10" value="3" label="Number of items deleted to consider"/>
        <conditional name="max_time_cond">
            <param name="max_time_param" type="select" label="Time out" help="Limit scan time">
                <option value="no" selected="True">no</option>
                <option value="yes" >yes</option>
            </param>
            <when value="yes">
                <param name="max_time" type="integer" min="5" max="120" value="10" label="minutes"/>
            </when>
            <when value="no"/>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_tsv" format="tabular" label="${tool.name}(${input_strategy.strategy})" />
    </outputs>
    <tests>
        <test>
            <!--   test 1   -->
            <param name="model" ftype="sbml" value="iAF1260.xml.gz" />
            <param name="pathway" ftype="sbml" value="butanol.xml" />
            <param name="medium" ftype="tabular" value="butanol.tsv" />
            <param name="biomass_rxn_id" value="BIOMASS_Ec_iAF1260_core_59p81M" />
            <param name="target_rxn_id" value="EX_1btol_e" />
            <param name="substrate_rxn_id" value="EX_glc__D_e" />
            <param name="max_time_param" value="yes"/>
            <param name="max_time" value="5"/>
            <output name="output_tsv" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="^reactions\tgenes\tsize\tfva_min\tfva_max\ttarget_flux\tbiomass_flux\tyield\tfitness$"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_TITLE@

This tool helps to identify gene's deletions in a biological model to optimize the reaction of a targeted compound.
The medium composition can be modified with a TSV file formatted as following: no header, with these columns "reaction id, lower_bound, upper_bound".
The strategies "ko" and "ou" find genes and reactions respectively to delete.

Disclaimer: if you want to annotate the genes with their names, your email address will be used by the library Biopython to request the NCBI website.

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