<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT">
    <description>Get an SBML model (BiGG)</description>
    <requirements>
        <requirement type="package" version="7.81.0">curl</requirement>
        <requirement type="package" version="1.11">gzip</requirement>
        <requirement type="package" version="5.19.2">python-libsbml</requirement>
        <requirement type="package" version="5.19.2">requests</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
        | gunzip > '$model';
        python '$__tool_directory__/'get_infos.py '$model' --hostid '$input' --comp '$compartments' --biomass '$biomass' --taxid '$taxid'
    ]]></command>
    <inputs>
        <param name="input" type="select" label="Strain">
            <option value="iCN718">Acinetobacter baumannii AYE (iCN718)</option>
            <option value="iYO844">Bacillus subtilis subsp. subtilis str. 168 (iYO844)</option>
            <option value="iRC1080">Chlamydomonas reinhardtii (iRC1080)</option>
            <option value="iCN900">Clostridioides difficile 630 (iCN900)</option>
            <option value="iHN637">Clostridium ljungdahlii DSM 13528 (iHN637)</option>
            <option value="iCHOv1_DG44">Cricetulus griseus (iCHOv1_DG44)</option>
            <option value="iCHOv1">Cricetulus griseus (iCHOv1)</option>
            <option value="iAF1260b">Escherichia coli str. K-12 substr. MG1655 (iAF1260b)</option>
            <option value="iAF1260">Escherichia coli str. K-12 substr. MG1655 (iAF1260)</option>
            <option value="iML1515" selected="true">Escherichia coli str. K-12 substr. MG1655 (iML1515)</option>
            <option value="iJO1366">Escherichia coli str. K-12 substr. MG1655 (iJO1366)</option>
            <option value="iJR904">Escherichia coli str. K-12 substr. MG1655 (iJR904)</option>
            <option value="e_coli_core">Escherichia coli str. K-12 substr. MG1655 (e_coli_core)</option>
            <option value="iAF987">Geobacter metallireducens GS-15 (iAF987)</option>
            <option value="iIT341">Helicobacter pylori 26695 (iIT341)</option>
            <option value="iAT_PLT_636">Homo sapiens (iAT_PLT_636)</option>
            <option value="Recon3D">Homo sapiens (Recon3D)</option>
            <option value="iAB_RBC_283">Homo sapiens (iAB_RBC_283)</option>
            <option value="RECON1">Homo sapiens (RECON1)</option>
            <option value="iYL1228">Klebsiella pneumoniae subsp. pneumoniae MGH 78578 (iYL1228)</option>
            <option value="iNF517">Lactococcus lactis subsp. cremoris MG1363 (iNF517)</option>
            <option value="iAF692">Methanosarcina barkeri str. Fusaro (iAF692)</option>
            <option value="iMM1415">Mus musculus (iMM1415)</option>
            <option value="iNJ661">Mycobacterium tuberculosis H37Rv (iNJ661)</option>
            <option value="iEK1008">Mycobacterium tuberculosis H37Rv (iEK1008)</option>
            <option value="iLB1027_lipid">Phaeodactylum tricornutum CCAP 1055/1 (iLB1027_lipid)</option>
            <option value="iAM_Pb448">Plasmodium berghei (iAM_Pb448)</option>
            <option value="iAM_Pc455">Plasmodium cynomolgi strain B (iAM_Pc455)</option>
            <option value="iAM_Pf480">Plasmodium falciparum 3D7 (iAM_Pf480)</option>
            <option value="iAM_Pk459">Plasmodium knowlesi strain H (iAM_Pk459)</option>
            <option value="iAM_Pv461">Plasmodium vivax Sal-1 (iAM_Pv461)</option>
            <option value="iJN746">Pseudomonas putida KT2440 (iJN746)</option>
            <option value="iJN1463">Pseudomonas putida KT2440 (iJN1463)</option>
            <option value="iND750">Saccharomyces cerevisiae S288C (iND750)</option>
            <option value="iMM904">Saccharomyces cerevisiae S288C (iMM904)</option>
            <option value="STM_v1_0">Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (STM_v1_0)</option>
            <option value="iYS1720">Salmonella pan-reactome (iYS1720)</option>
            <option value="iSB619">Staphylococcus aureus subsp. aureus N315 (iSB619)</option>
            <option value="iYS854">Staphylococcus aureus subsp. aureus USA300_TCH1516 (iYS854)</option>
            <option value="iJB785">Synechococcus elongatus PCC 7942 (iJB785)</option>
            <option value="iJN678">Synechocystis sp. PCC 6803 (iJN678)</option>
            <option value="iSynCJ816">Synechocystis sp. PCC 6803 (iSynCJ816)</option>
            <option value="iLJ478">Thermotoga maritima MSB8 (iLJ478)</option>
            <option value="iIS312">Trypanosoma cruzi Dm28c (iIS312)</option>
            <option value="iIS312_Trypomastigote">Trypanosoma cruzi Dm28c (iIS312_Trypomastigote)</option>
            <option value="iIS312_Epimastigote">Trypanosoma cruzi Dm28c (iIS312_Epimastigote)</option>
            <option value="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
        </param>
    </inputs>
    <outputs>
        <data name="model" format="sbml" label="${input}" />
        <data name="taxid" format="tsv" label="${input} (taxon id)" />
        <data name="compartments" format="tsv" label="${input} (compartments)" />
        <data name="biomass" format="tsv" label="${input} (biomass reactions)" />
    </outputs>
    <tests>
        <test>
        <!-- test 1: check if identical outputs are produced with iML1515 model input  -->
            <param name="input" value="iML1515" />
            <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
            <output name="taxid" md5="ec29688652dd49becf7be2a6c2469287"/>
            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>
            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
        </test>
    </tests>
    <help><![CDATA[
Pick SBML Model
=================

Download the selected SBML model fromg BiGG database.
    ]]></help>
    <creator>
        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
    </creator>
    <citations>
        <citation type="bibtex">
            @unpublished{get_sbml_model
                author = {Joan Hérisson},
                title = {{get_sbml_model}},
                url = {https://github.com/brsynth/},
            }
        </citation>
    </citations>
</tool>