comparison get_sbml_model.xml @ 2:fa893f77dc22 draft

planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f

1:ceffb29b60c9

<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.2" 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>
    </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' --comp '$compartments' --biomass '$biomass'
    ]]></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="iIS312_Amastigote">Trypanosoma cruzi Dm28c (iIS312_Amastigote)</option>
        </param>
    </inputs>
    <outputs>
        <data name="model" format="sbml" label="${input}" />
        <data name="compartments" format="tsv" label="${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="comp" 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>
</tool>

2:fa893f77dc22

<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>
    </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="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>