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comparison macros.xml @ 4:36c91ff33d70 draft

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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86
author iuc
date Sat, 15 Jun 2024 15:43:28 +0000
parents 33fac436dd54
children d6d746d0d1d0
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3:33fac436dd54 4:36c91ff33d70
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.2.0</token> 3 <token name="@TOOL_VERSION@">1.2.0</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">1</token>
5 <xml name="main_parameters"> 5 <xml name="main_parameters">
6 <conditional name="main_params"> 6 <conditional name="main_params">
7 <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?"> 7 <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
8 <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option> 8 <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option>
9 <option value="set_threshold">Specify threshold, estimate max ambiguous nts</option> 9 <option value="set_threshold">Specify threshold, estimate max ambiguous nts</option>
91 <param name="PCR_DV_CONC" type="float" min="0" value="2" label="Divalent cations mM conc." /> 91 <param name="PCR_DV_CONC" type="float" min="0" value="2" label="Divalent cations mM conc." />
92 <param name="PCR_DNTP_CONC" type="float" min="0" value="0.8" label="dNTP mM conc." /> 92 <param name="PCR_DNTP_CONC" type="float" min="0" value="0.8" label="dNTP mM conc." />
93 <param name="PCR_DNA_CONC" type="float" min="0" value="15" label="Primer nM conc." /> 93 <param name="PCR_DNA_CONC" type="float" min="0" value="15" label="Primer nM conc." />
94 </section> 94 </section>
95 <section name="penalty_multipliers" title="Primer penalties, multipliers and penalty cutoffs" expanded="false"> 95 <section name="penalty_multipliers" title="Primer penalties, multipliers and penalty cutoffs" expanded="false">
96 <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." /> 96 <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." />
97 <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." /> 97 <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." />
98 <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."/> 98 <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."/>
99 <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." /> 99 <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." />
100 <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."> 100 <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.">
101 <validator type="regex" message="Please specify a comma-separated list of integers"> *(\d+, *)*\d+ *$</validator> 101 <validator type="regex" message="Please specify a comma-separated list of integers"> *(\d+, *)*\d+ *$</validator>