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annotate macros.xml @ 0:462e62be07e1 draft

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planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
author iuc
date Sat, 27 Jan 2024 12:34:39 +0000
parents
children 80e18c0836e5
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462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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1 <?xml version="1.0"?>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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2 <macros>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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3 <token name="@TOOL_VERSION@">1.1.1</token>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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4 <token name="@VERSION_SUFFIX@">0</token>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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5 <xml name="main_parameters">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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6 <conditional name="main_params">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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7 <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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8 <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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9 <option value="set_threshold">Specify threshold, estimate max ambiguous nts</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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10 <option value="set_both">Specify values for both</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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11 </param>
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12 <when value="set_n_ambig">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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13 <param argument="--n-ambig" type="integer" min="0" value="2" label="Maximum number of ambiguous nucleotides per primer to be tolerated (default: 2)" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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14 <yield />
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15 </when>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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16 <when value="set_threshold">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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17 <param argument="--threshold" type="float" min="0.0" max="1.0" value="0.8" label="Threshold for consensus nucleotides" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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18 </when>
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19 <when value="set_both">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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20 <param argument="--threshold" type="float" min="0.0" max="1.0" value="0.8" label="Threshold for consensus nucleotides" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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21 <param argument="--n-ambig" type="integer" min="0" value="2" label="Maximum number of ambiguous nucleotides per primer to be tolerated" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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22 <yield />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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23 </when>
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24 </conditional>
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25 </xml>
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26 <xml name="amplicon_length_restrictions">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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27 <param argument="--opt-length" type="integer" min="1" value="1000" label="Optimal length of the amplicons" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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28 <param argument="--max-length" type="integer" min="1" value="1500" label="Maximal length of the amplicons" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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29 </xml>
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30 <xml name="blast_options">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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31 <conditional name="filter_blast_hits">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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32 <param name="choice" type="select" label="Avoid amplicons with off-target primer products?" help="This functionality requires a custom BLAST database of off-target sequences to check amplicon primer candidates against." >
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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33 <option value="no">No, don't consider off-target products</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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34 <option value="yes">Yes</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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35 </param>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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36 <when value="no" />
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37 <when value="yes">
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38 <param argument="--database" type="data" format="blastdbn" label="BLAST database" />
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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39 <conditional name="blast_advanced_cond">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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40 <param name="blast_advanced" type="select" label="Customize BLAST Settings?" help="Choosing Yes here, lets you overwrite advanced BLAST-related settings defined in varVAMP's default configuration file." >
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41 <option value="no">No, use varVAMP default settings</option>
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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42 <option value="yes">Yes</option>
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43 </param>
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44 <when value="no" />
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45 <when value="yes">
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46 <section name="blast_params" title="BLAST parameters">
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47 <param name="evalue" type="integer" min="0" value="5000" label="BLAST expect (E) value"/>
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48 <param name="reward" type="integer" min="0" value="1" label="BLAST reward (for a nucleotide match)"/>
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49 <param name="penalty" type="integer" max="0" value="-1" label="BLAST penalty (for a mismatch)"/>
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50 <param name="gapopen" type="integer" min="0" value="2" label="BLAST gapopen" help="Cost to open a gap"/>
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51 <param name="gapextend" type="integer" min="0" value="1" label="BLAST gapextend" help="Cost to extend a gap"/>
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52 </section>
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53 <section name="blast_hits_usage" title="varVAMP settings for handling BLAST hits">
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54 <param name="BLAST_MAX_DIFF" type="float" min="0" max="1" value="0.5" label="BLAST_MAX_DIFF" help="Minimal fraction of identity to primer to consider a BLAST hit an off-target primer binding site" />
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55 <param name="BLAST_SIZE_MULTI" type="float" min="1" value="2" label="BLAST_SIZE_MULTI" help="Disregard off-target amplicons with a length greater than the configured maximal length of target amplicons multiplied by this value" />
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56 <param name="BLAST_PENALTY" type="integer" min="0" value="50" label="BLAST_PENALTY" help="Extra penalty imposed on amplicons with off-target primer products; the default of 50 should be high enough to consider such amplicons only when no other amplicons without off-target products can be found." />
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57 </section>
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58 </when>
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59 </conditional>
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60 </when>
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61 </conditional>
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62 </xml>
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63 <xml name="customize_advanced">
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64 <conditional name="advanced_config">
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65 <param name="customize" type="select" label="Customize Advanced Settings?" help="Choosing Yes here, lets you overwrite advanced settings defined in varVAMP's default configuration file.">
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66 <option value="no">No, use defaults for advanced settings</option>
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67 <option value="yes">Yes</option>
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68 </param>
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69 <when value="no" />
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70 <when value="yes">
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71 <section name="basic_primer_params" title="Constraints on amplicon primers" expanded="false">
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72 <param name="PRIMER_TMP_min" type="integer" min="0" value="56" label="Minimal melting temperature"/>
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73 <param name="PRIMER_TMP_max" type="integer" min="0" value="63" label="Maximal melting temperature"/>
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74 <param name="PRIMER_TMP_opt" type="integer" min="0" value="60" label="Optimal melting temperature"/>
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75 <param name="PRIMER_GC_RANGE_min" type="integer" min="0" max="100" value="35" label="Minimal GC-content" />
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76 <param name="PRIMER_GC_RANGE_max" type="integer" min="0" max="100" value="65" label="Maximal GC-content" />
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77 <param name="PRIMER_GC_RANGE_opt" type="integer" min="0" max="100" value="50" label="Optimal GC-content" />
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78 <param name="PRIMER_SIZES_min" type="integer" min="1" value="18" label="Minimal primer size" />
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79 <param name="PRIMER_SIZES_max" type="integer" min="1" value="24" label="Maximal primer size" />
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80 <param name="PRIMER_SIZES_opt" type="integer" min="1" value="21" label="Optimal primer size" />
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81 <param name="PRIMER_MAX_POLYX" type="integer" min="1" value="4" label="Maximal length of polyX runs in primer" />
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82 <param name="PRIMER_MAX_DINUC_REPEATS" type="integer" min="0" value="4" label="Maximal length of dinucleotide repeats in primer" />
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83 <param name="PRIMER_GC_END_min" type="integer" min="0" max="5" value="1" label="Minimal number of GCs among the 3'-terminal 5 bases of the primer" />
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84 <param name="PRIMER_GC_END_max" type="integer" min="0" max="5" value="3" label="Maximal number of GCs among the 3'-terminal 5 bases of the probe" />
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85 <param name="PRIMER_MIN_3_WITHOUT_AMB" type="integer" min="0" value="3" label="Minimal length of 3'-end without ambiguous bases." />
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86 <param name="PRIMER_HAIRPIN" type="integer" min="0" value="47" label="Maximal melting temperature for secondary structures (hairpins) in primer" />
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87 <param name="PRIMER_MAX_DIMER_TMP" type="integer" min="0" value="47" label="Maximal melting temperature for primer dimers (homo- or heterodimers)" />
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88 </section>
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89 <yield />
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90 <section name="pcr_params" title="PCR Parameters" expanded="false">
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91 <param name="PCR_MV_CONC" type="float" min="0" value="100" label="Monovalent cations mM conc." />
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92 <param name="PCR_DV_CONC" type="float" min="0" value="2" label="Divalent cations mM conc." />
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93 <param name="PCR_DNTP_CONC" type="float" min="0" value="0.8" label="dNTP mM conc." />
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94 <param name="PCR_DNA_CONC" type="float" min="0" value="15" label="Primer nM conc." />
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95 </section>
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96 <section name="penalty_multipliers" title="Primer penalties, multipliers and penalty cutoffs" expanded="false">
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97 <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." />
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98 <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." />
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99 <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."/>
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100 <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." />
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101 <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.">
462e62be07e1 planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d
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102 <validator type="regex" message="Please specify a comma-separated list of integers"> *(\d+, *)*\d+ *$</validator>
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103 </param>
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104 <param name="PRIMER_PERMUTATION_PENALTY" type="float" min="0" value="0.1" label="Permutations penalty" help="For primers with ambiguous bases, permutations are the number of possible non-ambiguous primer sequences that the ambiguous sequence represents. Each individual permutation inflicts the penalty defined here." />
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105 </section>
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106 </when>
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107 </conditional>
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108 </xml>
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109 <xml name="primer_scheme_outputs">
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110 <param name="scheme_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Primer scheme outputs">
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111 <option value="primer_seqs" selected="true">Sequences of all designed oligos</option>
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112 <option value="primer_binding_sites" selected="true">Primer binding sites in BED format; includes primer penalties (lower is better) as the score column</option>
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113 <option value="amplicon_sites" selected="true">Amplicon locations in BED format; includes amplicon penalties (lower is better) in the score column</option>
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114 <option value="primer_details" selected="true">Primer details in tabular format</option>
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115 <yield />
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116 </param>
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117 </xml>
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118 <xml name="consensus_outputs">
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119 <param name="aln_cons_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Consensus sequence and alignment-related outputs">
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120 <option value="ambiguous_consensus" selected="true">The consensus sequence containing ambiguous nucleotides; this sequence is what positional information in primer scheme outputs is referring to!</option>
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121 <option value="majority_consensus">Consensus sequence without ambiguous nucleotide codes, but with the most prevalent nucleotide at each position instead.</option>
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122 <option value="alignment_cleaned">The preprocessed alignment used to build consensus sequences</option>
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123 </param>
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124 </xml>
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125 <xml name="graphical_outputs">
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126 <param name="plot_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Graphical outputs">
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127 <option value="amplicon_plot" selected="true">Amplicon design overview</option>
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128 <option value="per_base_mismatches" selected="true">Per-primer barplot of mismatches to input sequences</option>
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129 </param>
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130 </xml>
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131 <xml name="miscellaneous_outputs">
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132 <param name="misc_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Other/intermediate outputs" help="These outputs enable more complete tracing of steps performed by varVAMP and serve mostly debug purposes.">
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133 <option value="primer_regions">List of all candidate regions of the consensus sequence that were evaluated for primers in BED format</option>
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134 <yield />
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135 </param>
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136 </xml>
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137 </macros>
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138