comparison retropath2_wrapper.xml @ 12:da083c323f5c draft default tip

planemo upload for repository https://github.com/brsynth/retropath2_wrapper commit 96a30e92eab3144b924fdba7b63be10b218160a7

11:5f4a981d6bc3

    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
    </requirements>
    <stdio>
        <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" />
        <exit_code range="2" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" />
        <exit_code range="3" level="fatal" description="The InChI string is malformed" />
        <exit_code range="-1" level="warning" description="Source has been found in the sink" />
        <exit_code range="-2" level="warning" description="RetroPath2.0 has found no solution" />
        <exit_code range="-3" level="warning" description="Time limit reached" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m retropath2_wrapper
            '$sinkfile'
            '$rulesfile'

        </param>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="version" type="select" label="Workflow version" help="Retropath2.0 Workflow versions, formatted as 'r{year}{month}{day}' (the latest version 'r20220104' is used by default).">
                <option value="v9">v9</option>
                <option value="r20210127">r20210127</option>
                <option value="r20220104" selected="true">r20220104</option>
            </param>
            <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." />

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    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
    </requirements>
    <stdio>
        <!-- Fatal -->
        <exit_code range="1" level="fatal" description="Cannot find source-in-sink file" />
        <regex match="It seems that the target product is already in the chassis" source="both" level="fatal" description="It seems that the target product is already in the chassis" />
        <exit_code range="2" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" />
        <regex match="The following error occured" source="both" level="fatal" description="The following error occured" />
        <exit_code range="3" level="fatal" description="The InChI string is malformed" />
        <regex match="is not a valid InChI notation" source="both" level="fatal" description="is not a valid InChI notation" />
        <exit_code range="4" level="fatal" description="Sink file is malformed" />
        <regex match="The sink file is malformed" source="both" level="fatal" description="The sink file is malformed" />
        <!-- Warning -->
        <exit_code range="10" level="warning" description="Source has been found in the sink" />
        <regex match="Source has been found in the sink" source="both" level="warning" description="Source has been found in the sink" />
        <exit_code range="11" level="warning" description="RetroPath2.0 has found no solution" />
        <regex match="No solution has been found" source="both" level="warning" description="No solution has been found" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m retropath2_wrapper
            '$sinkfile'
            '$rulesfile'

        </param>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="version" type="select" label="Workflow version" help="Retropath2.0 Workflow versions, formatted as 'r{year}{month}{day}' (the latest version 'r20220104' is used by default).">
                <option value="v9">v9</option>
                <option value="r20210127">r20210127</option>
                <option value="r20220104">r20220104</option>
                <option value="r20220224" selected="true">r20220224</option>
            </param>
            <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." />