comparison get_sbml_model.xml @ 7:8dc4d3964ab5 draft

planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 09fcdb371be214b222a2e1c540d7c6e7489ca258

6:9b5947d48192

<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.4" profile="21.09" 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="2.29">requests</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($cond_src.from_src) == 'from_bigg'
            curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
        #else
            cp '${cond_src.input_file}' '$model' &&
        #end if
        python '$__tool_directory__/'get_infos.py
        '$model'
        --hostid '${cond_src.hostid}'
        --comp '$compartments'
        --biomass '$biomass'
        --taxid '$taxid'
    ]]></command>
    <inputs>
        <conditional name="cond_src">
            <param name="from_src" type="select" label="Select source">
                <option value="from_bigg" selected="True">Download model from BiGG</option>
                <option value="from_history">Select file from the History</option>
            </param>
            <when value="from_history">
                <param name="hostid" type="text" help="ID of the model">
                    <validator type="empty_field" message="An ID is required"/>
                </param>
                <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
            </when>
            <when value="from_bigg">
                 <param name="hostid" type="select" label="Strain">

                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="model" format="sbml" label="${cond_src.hostid}" />
        <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" />
        <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" />
        <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />
    </outputs>
    <tests>
        <test>
            <conditional name="cond_src">
                <param name="from_src" value="from_bigg" />
                <param name="hostid" value="iML1515" />
            </conditional>
            <output name="model" md5="9bf81d20cab5476700697ded95b716d1" />
            <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />
        </test>
        <test>
            <conditional name="cond_src">
                <param name="from_src" value="from_history" />
                <param name="hostid" value="e_coli_core" />
                <param name="input_file" value="e_coli_core.xml" />
            </conditional>
            <output name="model" md5="4574760460afe9e1b3388dc15f354706" />
            <output name="taxid" md5="6b35ad8a1c2b640af4ba738c2f5f876e" />
            <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
            <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
            </test>
    </tests>
    <help><![CDATA[

7:8dc4d3964ab5

<tool id="get_sbml_model" name="Pick SBML Model" version="0.1.0" profile="21.09" 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="2.29">requests</requirement>
        <requirement type="package" version="0.1.0">taxonid</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($cond_src.from_src) == 'from_bigg'
            curl -o - 'http://bigg.ucsd.edu/static/models/${cond_src.hostid}.xml.gz' | gunzip > '$model' &&
        #else
            python -m taxonid '${cond_src.hostname}' --output-file tmpfile &&
            echo "#ID" > '$taxid' &&
            cat tmpfile >> '$taxid' &&
        #end if
        echo "listdir:";
        ls;
        python '$__tool_directory__/'get_infos.py
            #if str($cond_src.from_src) == 'from_bigg'
                '$model'
                --taxid '$taxid'
            #else
                '${cond_src.input_file}'
            #end if
            --hostid '${cond_src.hostid}'
            --comp '$compartments'
            --biomass '$biomass'
    ]]></command>
    <inputs>
        <conditional name="cond_src">
            <param name="from_src" type="select" label="Select source">
                <option value="from_bigg" selected="True">Download model from BiGG</option>
                <option value="from_history">Select file from the History</option>
            </param>
            <when value="from_history">
                <param name="hostname" type="text" help="Fullname of the model">
                    <validator type="empty_field" message="The fullname of the organism is required"/>
                </param>
                <param name="hostid" type="text" help="ID of the model">
                    <validator type="empty_field" message="ID of the organism is required"/>
                </param>
                <param name="input_file" type="data" format="sbml,xml" label="SBML model" help="An SBML file is expected"/>
            </when>
            <when value="from_bigg">
                 <param name="hostid" type="select" label="Strain">

                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="model" format="sbml" label="${cond_src.hostid}">
            <filter>cond_src['from_src'] == 'from_bigg'</filter>
        </data>
        <data name="taxid" format="tsv" label="${cond_src.hostid} (taxon id)" />
        <data name="compartments" format="tsv" label="${cond_src.hostid} (compartments)" />
        <data name="biomass" format="tsv" label="${cond_src.hostid} (biomass reactions)" />
    </outputs>
    <tests>
        <test>
            <param name="from_src" value="from_bigg" />
            <param name="hostid" value="iML1515" />
            <output name="model" md5="9bf81d20cab5476700697ded95b716d1" />
            <output name="taxid" md5="7c62bd818057838b3557c8d87cca47fc" />
            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236" />
            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06" />
        </test>
        <test>
            <conditional name="cond_src">
                <param name="from_src" value="from_history" />
                <param name="hostname" value="Escherichia coli str. K-12 substr. MG1655" />
                <param name="hostid" value="e_coli_core" />
                <param name="input_file" value="e_coli_core.xml" />
            </conditional>
            <output name="taxid" md5="ee08b511771328e6254775a51779d421" />
            <output name="compartments" md5="71dc18974a12e9bb75bb2c4cffd13edf" />
            <output name="biomass" md5="d10baa335181450c7bffa9b4ca01754a" />
            </test>
    </tests>
    <help><![CDATA[