<macros>
    <!--  GLOBAL  -->
    <token name="@TOOL_VERSION@">3.2.2</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@LICENSE@">MIT</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">straindesign</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <regex match="WARNING" level="warning" />
            <regex match="ERROR" level="fatal" />
        </stdio>
    </xml>
    <xml name="citation">
        <citations>
            <citation type="doi">10.1038/s41467-022-32661-x</citation>
        </citations>
    </xml>
    <xml name="creator">
        <creator>
            <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
        </creator>
    </xml>
    <xml name="env_variables">
        <environment_variables>
            <environment_variable name="XDG_CACHE_HOME">\$_GALAXY_JOB_TMP_DIR</environment_variable>
            <environment_variable name="USERNAME">\$__user_email__</environment_variable>
        </environment_variables>
    </xml>

    <!--  CMDLINE  -->
<token name="@CMD_INPUT_MODEL@"><![CDATA[
--input-model-file '$model'
]]></token>
<token name="@CMD_INPUT_PATHWAY@"><![CDATA[
#if $pathway
--input-pathway-file '$pathway'
#end if
]]></token>
<token name="@CMD_INPUT_MEDIUM@"><![CDATA[
#if $medium
    --input-medium-file '$medium'
#end if
]]></token>
<token name="@CMD_BIOMASS_RXN_ID@"><![CDATA[
--biomass-rxn-id '$biomass_rxn_id'
]]></token>
<token name="@CMD_TARGET_RXN_ID@"><![CDATA[
--target-rxn-id '$target_rxn_id'
]]></token>

    <!--  INPUT  -->
    <xml name="input_model_sbml">
        <param name="model" type="data" format="sbml" label="Model" help="SBML input file, model"/>
    </xml>
    <xml name="input_pathway_sbml">
        <param name="pathway" type="data" format="sbml" optional="True" label="Pathway" help="SBML input file, containing heterologous pathway"/>
    </xml>
    <xml name="input_medium_tsv">
        <param name="medium" type="data" format="tabular" optional="True" label="Medium file" help="TSV input file, no header, with three columns: reaction_id, lower_bound, upper_bound"/>
    </xml>
    <xml name="input_biomass_rxn_id">
        <param name="biomass_rxn_id" type="text" value="" label="Biomass reaction ID" help="Reaction ID contains no special characters">
            <validator type="empty_field" message="Biomass reaction ID is required"/>
            <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
        </param>
    </xml>
    <xml name="input_target_rxn_id">
        <param name="target_rxn_id" type="text" value="" label="Target reaction ID" help="Reaction ID contains no special characters">
            <validator type="empty_field" message="Target reaction ID is required"/>
            <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
        </param>
    </xml>
    <xml name="input_substrate_rxn_id">
        <param name="substrate_rxn_id" type="text" value="" label="Substrate reaction ID" help="Reaction ID contains no special characters">
            <validator type="empty_field" message="Target reaction ID is required"/>
            <validator type="regex" message="No special characters allowed">^(?:[a-zA-Z_])(?:[\w.-])*$</validator>
        </param>
    </xml>

    <!--  HELP -->
<token name="@HELP_TITLE@"><![CDATA[
StrainDesign
============
]]></token>
<token name="@HELP_LINK@"><![CDATA[
Project Links
-------------

* `straindesign <https://github.com/brsynth/straindesign>`_
* `cameo <https://github.com/biosustain/cameo>`_
]]></token>
</macros>