comparison retropath2_wrapper.xml @ 11:5f4a981d6bc3 draft

planemo upload for repository https://github.com/brsynth/retropath2_wrapper commit b7e98c7f0ee70edd536215e3dfe0cd66957e6dae

10:fe60c5bd7a9d

<tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
    <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">3.1.1</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
    </requirements>
    <stdio>

            --topx '$adv.topx'
            --dmin '$adv.dmin'
            --dmax '$adv.dmax'
            --mwmax_source '$adv.mwmax_source'
            --kinstall "\${TMPDIR:-.}"
            --msc_timeout '$adv.timeout' &&
        if compgen -G 'out/*_scope.csv' > /dev/null; then
            cp out/*_scope.csv '$Reaction_Network';
        else
            cp out/results.csv '$Reaction_Network';

            <param name="topx" type="integer" value="100" min="1" max="1000" label="TopX" help="The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm." />
            <param name="dmin" type="integer" value="0" min="0" max="1000" label="Minimum rule diameter" help="Minimum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules." />
            <param name="dmax" type="integer" value="1000" min="0" max="1000" label="Maximum rule diameter" help="Maximum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules."/>
            <param name="mwmax_source" type="integer" value="1000" min="0" max="2000" label="Molecular weight of source (Da)" help="The molecular weight cutoff (in Da), above which initial source (ie target) and intermediate compounds will be filtered out." />
            <param name="timeout" type="integer" value="60" min="30" max="600" label="Timeout (min)" help="Maximal time of RetroPath2.0 execution (60 minutes by default)." />
        </section>
    </inputs>
    <outputs>
        <data name="Reaction_Network" format="csv" label="${tool.name}" >
            <actions>

11:5f4a981d6bc3

<tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
    <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">3.2.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
    </requirements>
    <stdio>

            --topx '$adv.topx'
            --dmin '$adv.dmin'
            --dmax '$adv.dmax'
            --mwmax_source '$adv.mwmax_source'
            --kinstall "\${TMPDIR:-.}"
            #if str($adv.network) == "true":
                --no-network
            #end if
            --msc_timeout '$adv.timeout' &&
        if compgen -G 'out/*_scope.csv' > /dev/null; then
            cp out/*_scope.csv '$Reaction_Network';
        else
            cp out/results.csv '$Reaction_Network';

            <param name="topx" type="integer" value="100" min="1" max="1000" label="TopX" help="The maximal number of intermediate compounds to use as new starting points for a next iteration of the retrosynthesis algorithm." />
            <param name="dmin" type="integer" value="0" min="0" max="1000" label="Minimum rule diameter" help="Minimum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules." />
            <param name="dmax" type="integer" value="1000" min="0" max="1000" label="Maximum rule diameter" help="Maximum rule diameter of the sphere including the atoms around the reacting center. The higher is the diameter, the more specific are the rules."/>
            <param name="mwmax_source" type="integer" value="1000" min="0" max="2000" label="Molecular weight of source (Da)" help="The molecular weight cutoff (in Da), above which initial source (ie target) and intermediate compounds will be filtered out." />
            <param name="timeout" type="integer" value="60" min="30" max="600" label="Timeout (min)" help="Maximal time of RetroPath2.0 execution (60 minutes by default)." />
            <param name="network" type="boolean" checked="false" label="Do not use network" />
        </section>
    </inputs>
    <outputs>
        <data name="Reaction_Network" format="csv" label="${tool.name}" >
            <actions>