comparison rrparser.xml @ 11:ac6c16ae1f88 draft default tip

planemo upload for repository https://github.com/brsynth/rrparser commit 01d525eee7e9fe6c9a3d89101c465c99928a71c2

10:3449d7bfee20

<tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
    <description>Retrieve the reaction rules from RetroRules</description>
    <macros>
        <token name="@VERSION_SUFFIX@">3</token>
        <token name="@TOOL_VERSION@">2.7.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
    </requirements>

                    <option value="in">EC numbers to keep</option>
                    <option value="out">EC numbers to remove</option>
                </param>
                <when value="no" />
                <when value="in">
                    <param name="input_ec_in" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
                </when>
                <when value="out">
                    <param name="input_ec_out" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
                </when>
            </conditional>
            <param argument="--diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules" help=" Diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules">
                <option selected="true" value="2">2</option>
                <option selected="true" value="4">4</option>

                <param name="file" value="rules_in.csv" />
            </conditional>
            <section name="adv">
                <conditional name="input_conditional_ec">
                    <param name="input_type" value="in"/>
                    <param name="input_ec_in" value="ec.csv"/>
                </conditional>
            </section>
            <output name="out_rules" file="test.4.output.csv" ftype="csv" compare="diff"/>
        </test>
        <test>
            <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -ecx ec.csv -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile test.5.output.csv -->
            <conditional name="rules">
                <param name="type" value="rules-file"/>
                <param name="file" value="rules_in.csv" />
            </conditional>
            <section name="adv">
                <conditional name="input_conditional_ec">
                    <param name="input_type" value="out"/>
                    <param name="input_ec_out" value="ec.csv"/>
                </conditional>
            </section>
            <output name="out_rules" file="test.5.output.csv" ftype="csv" compare="diff"/>
        </test>
        <test>

11:ac6c16ae1f88

<tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
    <description>Retrieve the reaction rules from RetroRules</description>
    <macros>
        <token name="@VERSION_SUFFIX@">4</token>
        <token name="@TOOL_VERSION@">2.7.0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
    </requirements>

                    <option value="in">EC numbers to keep</option>
                    <option value="out">EC numbers to remove</option>
                </param>
                <when value="no" />
                <when value="in">
                    <param name="input_ec_in" type="data" format="txt" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
                </when>
                <when value="out">
                    <param name="input_ec_out" type="data" format="txt" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
                </when>
            </conditional>
            <param argument="--diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules" help=" Diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules">
                <option selected="true" value="2">2</option>
                <option selected="true" value="4">4</option>

                <param name="file" value="rules_in.csv" />
            </conditional>
            <section name="adv">
                <conditional name="input_conditional_ec">
                    <param name="input_type" value="in"/>
                    <param name="input_ec_in" value="ec.txt"/>
                </conditional>
            </section>
            <output name="out_rules" file="test.4.output.csv" ftype="csv" compare="diff"/>
        </test>
        <test>
            <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -ecx ec.txt -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile test.5.output.csv -->
            <conditional name="rules">
                <param name="type" value="rules-file"/>
                <param name="file" value="rules_in.csv" />
            </conditional>
            <section name="adv">
                <conditional name="input_conditional_ec">
                    <param name="input_type" value="out"/>
                    <param name="input_ec_out" value="ec.txt"/>
                </conditional>
            </section>
            <output name="out_rules" file="test.5.output.csv" ftype="csv" compare="diff"/>
        </test>
        <test>