comparison macros.xml @ 4:36c91ff33d70 draft default tip

planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86

3:33fac436dd54

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.2.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="main_parameters">
        <conditional name="main_params">
            <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
                <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option>
                <option value="set_threshold">Specify threshold, estimate max ambiguous nts</option>

                    <param name="PCR_DV_CONC" type="float" min="0" value="2" label="Divalent cations mM conc." />
                    <param name="PCR_DNTP_CONC" type="float" min="0" value="0.8" label="dNTP mM conc." />
                    <param name="PCR_DNA_CONC" type="float" min="0" value="15" label="Primer nM conc." />
                </section>
                <section name="penalty_multipliers" title="Primer penalties, multipliers and penalty cutoffs" expanded="false">
                    <param name="PRIMER_TM_PENALTY" type="float" min="0" max="10" value="2" label="Temperature penalty multiplier" help="Each °C deviation of primer melting temperature from the configured optimal melting temperature inflicts a penalty of this size." />
                    <param name="PRIMER_GC_PENALTY" type="float" min="0" value="0.2" label="GC-content penalty multiplier" help="Each % deviation of primer GC-content from the configured optimal GC-content inflicts a penalty of this size." />
                    <param name="PRIMER_SIZE_PENALTY" type="float" min="0" value="0.5" label="Primer size penalty multiplier" help="Each base deviation of primer length from the configured optimal length inflicts a penalty of this size."/>
                    <param name="PRIMER_MAX_BASE_PENALTY" type="integer" min="0" value="10" label="Maximal primer base penalty" help="Primer base penalty is the sum of the primer's temperature, GC-content and size penalties as defined above. If that base penalty exceeds the maximum defined here, the candidate primer gets discarded and is not considered further." />
                    <param name="PRIMER_3_PENALTY" type="text" value="32, 16, 8, 4, 2" optional="false" label="3' mismatch penalties" help="This comma-separated list of integers, defines the extra penalties associated with mismatches at the last, second-last, third-last, etc. base from the 3'-end of the primer. These extra penalties are added after applying the maximal base penalty threshold above.">
                        <validator type="regex" message="Please specify a comma-separated list of integers"> *(\d+, *)*\d+ *$</validator>

4:36c91ff33d70

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.2.0</token>
    <token name="@VERSION_SUFFIX@">1</token>
    <xml name="main_parameters">
        <conditional name="main_params">
            <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
                <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option>
                <option value="set_threshold">Specify threshold, estimate max ambiguous nts</option>

                    <param name="PCR_DV_CONC" type="float" min="0" value="2" label="Divalent cations mM conc." />
                    <param name="PCR_DNTP_CONC" type="float" min="0" value="0.8" label="dNTP mM conc." />
                    <param name="PCR_DNA_CONC" type="float" min="0" value="15" label="Primer nM conc." />
                </section>
                <section name="penalty_multipliers" title="Primer penalties, multipliers and penalty cutoffs" expanded="false">
                    <param name="PRIMER_TM_PENALTY" type="float" min="0" value="2" label="Temperature penalty multiplier" help="Each °C deviation of primer melting temperature from the configured optimal melting temperature inflicts a penalty of this size." />
                    <param name="PRIMER_GC_PENALTY" type="float" min="0" value="0.2" label="GC-content penalty multiplier" help="Each % deviation of primer GC-content from the configured optimal GC-content inflicts a penalty of this size." />
                    <param name="PRIMER_SIZE_PENALTY" type="float" min="0" value="0.5" label="Primer size penalty multiplier" help="Each base deviation of primer length from the configured optimal length inflicts a penalty of this size."/>
                    <param name="PRIMER_MAX_BASE_PENALTY" type="integer" min="0" value="10" label="Maximal primer base penalty" help="Primer base penalty is the sum of the primer's temperature, GC-content and size penalties as defined above. If that base penalty exceeds the maximum defined here, the candidate primer gets discarded and is not considered further." />
                    <param name="PRIMER_3_PENALTY" type="text" value="32, 16, 8, 4, 2" optional="false" label="3' mismatch penalties" help="This comma-separated list of integers, defines the extra penalties associated with mismatches at the last, second-last, third-last, etc. base from the 3'-end of the primer. These extra penalties are added after applying the maximal base penalty threshold above.">
                        <validator type="regex" message="Please specify a comma-separated list of integers"> *(\d+, *)*\d+ *$</validator>