| Next changeset 1:80e18c0836e5 (2024-04-05) |
|
Commit message:
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d |
|
added:
macros.xml test-data/ambiguous_consensus.fasta test-data/hepatitis_e_aln_shrunk.fasta test-data/test1.log test-data/test2.log test-data/test3.log test-data/test4.log varvamp.xml |
| b |
| diff -r 000000000000 -r 462e62be07e1 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Jan 27 12:34:39 2024 +0000 |
| b |
| b'@@ -0,0 +1,138 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@TOOL_VERSION@">1.1.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="main_parameters">\n+ <conditional name="main_params">\n+ <param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">\n+ <option value="set_n_ambig">Specify max ambiguous nts, estimate suitable threshold</option>\n+ <option value="set_threshold">Specify threshold, estimate max ambiguous nts</option>\n+ <option value="set_both">Specify values for both</option>\n+ </param>\n+ <when value="set_n_ambig">\n+ <param argument="--n-ambig" type="integer" min="0" value="2" label="Maximum number of ambiguous nucleotides per primer to be tolerated (default: 2)" />\n+ <yield />\n+ </when>\n+ <when value="set_threshold">\n+ <param argument="--threshold" type="float" min="0.0" max="1.0" value="0.8" label="Threshold for consensus nucleotides" />\n+ </when>\n+ <when value="set_both">\n+ <param argument="--threshold" type="float" min="0.0" max="1.0" value="0.8" label="Threshold for consensus nucleotides" />\n+ <param argument="--n-ambig" type="integer" min="0" value="2" label="Maximum number of ambiguous nucleotides per primer to be tolerated" />\n+ <yield />\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="amplicon_length_restrictions">\n+ <param argument="--opt-length" type="integer" min="1" value="1000" label="Optimal length of the amplicons" />\n+ <param argument="--max-length" type="integer" min="1" value="1500" label="Maximal length of the amplicons" />\n+ </xml>\n+ <xml name="blast_options">\n+ <conditional name="filter_blast_hits">\n+ <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." >\n+ <option value="no">No, don\'t consider off-target products</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <param argument="--database" type="data" format="blastdbn" label="BLAST database" />\n+ <conditional name="blast_advanced_cond">\n+ <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." >\n+ <option value="no">No, use varVAMP default settings</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <when value="no" />\n+ <when value="yes">\n+ <section name="blast_params" title="BLAST parameters">\n+ <param name="evalue" type="integer" min="0" value="5000" label="BLAST expect (E) value"/>\n+ <param name="reward" type="integer" min="0" value="1" label="BLAST reward (for a nucleotide match)"/>\n+ <param name="penalty" type="integer" max="0" value="-1" label="BLAST penalty (for a mismatch)"/>\n+ <param name="gapopen" type="integer" min="0" value="2" label="BLAST gapopen" help="Cost to open a gap"/>\n+ <param name="gapextend" type="integer" min="0" value="1" label="BLAST gapextend" help="Cost to extend a gap"/>\n+ </section>\n+ <section name="blast_hits_usage" title="varVAMP settings for handling BLAST hits">\n+ <param name="BLAST_MAX_DIFF" type="float" min='..b'pe="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."/>\n+ <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." />\n+ <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.">\n+ <validator type="regex" message="Please specify a comma-separated list of integers"> *(\\d+, *)*\\d+ *$</validator>\n+ </param>\n+ <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." />\n+ </section>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="primer_scheme_outputs">\n+ <param name="scheme_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Primer scheme outputs">\n+ <option value="primer_seqs" selected="true">Sequences of all designed oligos</option>\n+ <option value="primer_binding_sites" selected="true">Primer binding sites in BED format; includes primer penalties (lower is better) as the score column</option>\n+ <option value="amplicon_sites" selected="true">Amplicon locations in BED format; includes amplicon penalties (lower is better) in the score column</option>\n+ <option value="primer_details" selected="true">Primer details in tabular format</option>\n+ <yield />\n+ </param>\n+ </xml>\n+ <xml name="consensus_outputs">\n+ <param name="aln_cons_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Consensus sequence and alignment-related outputs">\n+ <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>\n+ <option value="majority_consensus">Consensus sequence without ambiguous nucleotide codes, but with the most prevalent nucleotide at each position instead.</option>\n+ <option value="alignment_cleaned">The preprocessed alignment used to build consensus sequences</option>\n+ </param>\n+ </xml>\n+ <xml name="graphical_outputs">\n+ <param name="plot_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Graphical outputs">\n+ <option value="amplicon_plot" selected="true">Amplicon design overview</option>\n+ <option value="per_base_mismatches" selected="true">Per-primer barplot of mismatches to input sequences</option>\n+ </param>\n+ </xml>\n+ <xml name="miscellaneous_outputs">\n+ <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.">\n+ <option value="primer_regions">List of all candidate regions of the consensus sequence that were evaluated for primers in BED format</option>\n+ <yield />\n+ </param>\n+ </xml>\n+</macros>\n+\n' |
| b |
| diff -r 000000000000 -r 462e62be07e1 test-data/ambiguous_consensus.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ambiguous_consensus.fasta Sat Jan 27 12:34:39 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +>ambiguous_consensus +tatcccgtrtycaractgayatccttattaayytgatgcaaccycgrcagcttgtkttccgrccygaagtyytstggaaycayccgatccagcgrgtyatacataatgagctggagcartactgccgwgcycgygctggycgytgyctkgargtkggsgcycayccaagatcyatyaatgayaacccyaatgtyytgcaccggtgcttyctycgcccggtyggdagagaygtmcagcgytggtaytcygccccsacycgyggyccagcggcyaaytgccgccgytcygcgctacgyggyytgccccctgtcgaycgyacmtaytgcttcgacgggttytcccgctgcgcytttgccgctgagacyggratygctttataytcactrcatgacctytggccytcggaygtygcggaggcya |
| b |
| diff -r 000000000000 -r 462e62be07e1 test-data/hepatitis_e_aln_shrunk.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hepatitis_e_aln_shrunk.fasta Sat Jan 27 12:34:39 2024 +0000 |
| b |
| b'@@ -0,0 +1,1104 @@\n+>MF444058.1\n+tatctcgtgttcaaactgagatccttattaacctgatgcaaccccggcagctcgtgtttc\n+ggcctgaagtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat\n+actgccgagcccgcgctggccgttgtcttgaggtgggcgctcacccaagatctattaatg\n+acaaccccaatgtcctacaccggtgctttctccgcccggttgggagagacgtccagcgct\n+ggtattccgcccccacccgtggtccagcggccaattgccgccgctctgcgctacgcggct\n+tgccccctgtcgatcgtacatattgcttcgatgggttttcccgctgcgcctttgccgccg\n+agaccgggatcgctttatactcactgcatgacctttggccctcggacgttgcggaggcta\n+>MN646693.1\n+tatctcgtattcagactgatatccttattaacctgatgcaacctcggcagcttgttttcc\n+ggcctgaagttctctggaatcacccgatccagcgagttatacataatgagctggagcaat\n+actgccgagcccgcgctggccgctgccttgaggtgggcgctcacccaagatccatcaatg\n+ataaccccaatgttctgcaccggtgctttctccgcccggttggcagagacgtccagcgct\n+ggtactccgcccccactcgtggtccagcggctaactgccgccgctctgcgctacgtggtt\n+tgccccctgtcgatcgtacatattgctttgacgggttctcccgctgcgcctttgccgctg\n+agaccgggattgctttatactcactgcacgacctttggccctcggacgttgcggaggcca\n+>KT591534.1\n+tatctcgtgtccaaactgatatccttattcacttgatgcaacctcggcagcttgtgttcc\n+gacctgaagtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat\n+actgccgggcccgcgccggccgctgtcttgaggtgggcgctcacccaagatctattaatg\n+ataaccccaatgttctgcaccggtgcttcctccgcccggtcggaagagacgtccagcgtt\n+ggtactctgcccccactcgtggcccagcggctaactgccgccgctctgcgctacgtggtt\n+tgccccctgtcgatcgcacatactgcttcgacgggttttcccgctgcgcttttgccgcag\n+agaccgggattgctctgtactcactgcatgatctttggccctcggacgttgcggaggcta\n+>KC166971.1\n+tatcccgtgttcaaactgatatccttatyaacttgatgcaacctcgacagcttgtgttcc\n+ggcccgaagtcctctggaatcatccgatccagcgagttatacataatgagctggagcaat\n+actgccgrgcccgcgctggccgttgtcttgaagtgggygcccacccaagatctattaatg\n+ataaccccaatgttytgcaccggtgctttctccgcccggttggaagagacgtccagcgct\n+ggtattcygcccccactcgyggtccagcggctaattgccgccgttctgcgctacgcggtt\n+tgccccctgtcgaccgcacgtattgcttcgacgggttctcccgctgcgcctttgccgctg\n+agaccgggattgctttatactcactgcatgacctttggccttcggatgtcgcggaggcta\n+>MF444034.1\n+tatcccgtgttcaaactgaaatccttattaacctgatgcaacctcgacagcttgtgttcc\n+ggcccgaagtcctctggaatcatccgatccagcgagttatacacaatgagctggagcaat\n+actgccgagcccgcgctggccgttgtcttgaagtgggcgcccatccaagatctattaatg\n+ataaccccaatgttctgcaccggtgctttctccgcccggttggtagagacgtccagcgct\n+ggtattccgcccccactcgtggcccagcggctaattgccgccgttctgcgttacgcggct\n+tgccccctgtcgaccgcacatattgcttcgacgggttctcccgctgcgcctttgccgctg\n+agaccgggatcgctttatactcactgcatgacctttggccttcggatgttgcggaggcta\n+>MF444119.1\n+tatcccgtgtccaaactgatatccttattaacttgatgcaacctcgacagcttgtgttcc\n+ggcccgaagtcttctggaatcatccgatccagcgagttatacataatgagctggagcagt\n+actgccgagcccgcgctggccgttgtcttgaagtgggcgcccacccaagatctattaatg\n+ataaccccaatgttctgcaccggtgctttcttcgcccggttggaagagacgtccagcgct\n+ggtactccgcccccactcgtggcccagcggctaattgccgccgttccgcgctacgcggct\n+taccccctgtcgaccgcacatattgcttcgacgggttttcccgctgcgcctttgccgctg\n+agaccgggatcgctttatactcactgcatgacctttggccttcggatgtcgcggaggcta\n+>MF444054.1\n+tatcccgtatccagactgatatcctcattaacctgatgcaaccccggcagcttgttttcc\n+ggcctgaagttctctggaatcacccgatccagcgggttatacataatgagttggagcaat\n+actgccgagcccgcgctggccgctgtcttgaggtgggcgctcacccaagatccatcaatg\n+ataaccccaatgttctgcaccggtgctttctccgcccggtcggtagagacgtccagcgct\n+ggtattctgcccccactcgtggcccggcggctaactgccgtcgctctgcgctacgtggtt\n+tgccccctgtcgatcgtacatactgcttcgacgggttttcccgctgtgcttttgctgctg\n+agaccgggattgctttatactcactgcatgacctttggccctcggacgttgcggaggcca\n+>MN646691.1\n+tatcccgtgcccagactgatatccttataaacctgatgcaaccccggcagctcgtgtttc\n+gtcccgaagttttgtggaaccacccgatccagcgagtcatacacaatgagctggaacagt\n+attgccgtgctcgtgctggtcgctgtctggaggtgggggctcatccaagatctattaatg\n+acaatcctaatgtcctgcatcggtgctttcttcgcccggttgggagagacgtacagcgct\n+ggtactctgccccgactcgcggtccagcggctaactgccgccgctctgcgttacgtggcc\n+tgccccctgtcgatcgtacctactgcttcgacgggttttcccgttgcgcatttgccgctg\n+agactggaattgccctgtactcattacatgacctctggcccgcggatgtcgcggaagcca\n+>MN646690.1\n+tatcccgtgcccagactgatatccttataaacctgatgcaaccccggcagctcgtgtttc\n+gtcccgaagttttgtggaaccacccgatccagcgagtcatacacaatgagctggaacagt\n+attgccgtgctcgtgctggtcgctgtctggaggtgggggctcatccaagatctattaatg\n+acaatcctaatgtcctgcatcggtgctttcttcgcccggttgggagagacgtacagcgct\n+ggtactctgccccgactcgcggtccagcggctaactgccgccgctctgcgttacgtggcc\n+tgccccctgtcgatcgtacctactgcttcgacgggttttcccgttgcgcatttgccgctg\n+agactggaattgccctgt'..b'tcaaactgacatccttatcaacttgatgcaaccccggcagcttgtttttc\n+gacctgaagttctctggaaccatccgatccagcgagttatacataacgagctggagcagt\n+actgccgagctcgtgctggtcgctgccttgaggtgggcgcccacccacgatccattaatg\n+ataaccccaatgttttgcaccggtgctttctccgcccggttggaagagatgtccagcgct\n+ggtactctgcccctactcgtggtccagcggccaactgccgccgttccgcgttacgtggcc\n+tgccccctgtcgatcgcacatactgtttcgacgggttttcccgctgcacctttgctgctg\n+agaccggaatcgctttatactcactgcatgatctatggccatcggacgttgcagaggcta\n+>MF444080.1\n+tatcccgtgtgcaaactgacatccttattaacctgatgcaaccccggcagctcgtgtttc\n+ggcctgaagttttctggaaccacccgatccagcgggtcatacataacgagctagagcaat\n+actgccgagctcgcgctggccgctgccttgaggtgggtgctcacccgaggtccattaatg\n+ataatcctaatgtcctgcaccggtgcttccttcgtccagtcgggagagatgtccagcgtt\n+ggtattctgcccccactcgcggcccagcggctaactgccgtcgctccgcactacgtggtt\n+tgcctcctgtcgaccgcacatactgcttcgacgggttctcccgctgtgctttcgccgctg\n+agaccggaatcgccttatattcactgcatgacctctggccttcggacgttgcggaggcca\n+>MF444053.1\n+tatcccgtgttcagaccgatatccttattaatctgatgcaacctcggcagctcgttttcc\n+ggcctgaagtcttctggaaccatccaattcagcgagtcatacataatgagttggagcaat\n+actgccgggcccgtgccggccgctgcctagaagtaggcgctcacccgaggtccatcaatg\n+acaatcctaatgtcctgcaccggtgctttcttcgcccggttggcagagatgttcagcgct\n+ggtattctgctcctactcgtggtccggcggccaattgccgtcgttctgcgctccgcggtc\n+taccccccgttgatcgcacttactgtttcgacgggttttcccgctgcgcttttgccgccg\n+agaccgggattgctttatactcactacatgacctctggccttcggacgttgcggaggcca\n+>MF444144.1\n+tatcccgtgttcaaactgacatccttattaacctgatgcaaccccggcagcttgtgttcc\n+gacctgaggtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat\n+actgccgagcccgcgctggccgctgccttgaggtgggcgctcacccgaggtctatcaatg\n+ataaccctaatgtcctgcaccggtgcttccttcgcccggttggaagagacgtccagcgct\n+ggtattctgcccctacccgtggaccagcggccaactgccgccgttctgcgcttcgcggtt\n+tgccccctgtcgatcgcacatactgcttcgatgggttctctcgctgcgctttcgccgctg\n+agaccgggattgctttatactcactgcatgacctctggccttcggacgttgcggaggcca\n+>KF922359.1\n+tgtcccgtgttcagaccgatattcttatcaatttgatgcaaccccggcagcttgtatttc\n+gccctgaagttctgtggaaccatccgattcagcgagttatacataatgagctagagcagt\n+attgccgtgctcgtgctggccgctgcctggaggtcggggctcatccaagatctattaatg\n+acaaccctaatgttttgcaccggtgcttcctccgtccggtcgggagggatgtccagcgct\n+ggtacactgcaccgactcgcggcccggcggctaactgccgccgctccgcgttacgtggcc\n+taccccctgtcgatcgtacctactgtttcgacgggttttcccgctgcgcctttgccgccg\n+agactggaattgccttatattcactacatgacctctggcctgcggatgttgcagaggcca\n+>MF444062.1\n+tatcccgtgtccagactgatatccttattaacttgatgcaaccccggcagcttgtgttcc\n+gacctgaagttctctggaaccatccaatccagcgagtgatacataatgaactggagcaat\n+actgccgagcccgtgctggccgttgtcttgaggtgggcgcccacccaagatccatcaacg\n+ataaccctaatgttctgcatcggtgctttctccgcccggttggaagagacgtccagcgct\n+ggtactctgcccccacccgtggtccagcggccaactgccgccgttctgcgctgcgtggtt\n+tgcctcctgtcgatcgcacatactgcttcgacgggttttcccgctgcgcctttgcagctg\n+agaccgggatcgctttatactcgctgcatgatctttggccctcggacgttgcggaggcta\n+>MF444118.1\n+tatcccgtgtccagactgacatccttattaatctgatgcaaccccggcagcttgtgttcc\n+gacctgaagtcctctggaaccatccgattcagcgagtcatacataatgagctggagcaat\n+actgccgagcccgcgctggccgctgtcttgaggtgggcgcccacccaagatctattaatg\n+ataaccccaacgttctgcaccggtgctttctccgcccggtcgggagagacgtccagcgct\n+ggtattctgcccctactcgcggtccagcggccaattgccgccgttctgcgctacgcggtt\n+tgccccctgtcgaccgcacatactgcttcgacgggttttcccgctgcgctttcgccgctg\n+agaccgggatcgccttatactcgctgcatgacctttggccctcggacgttgcggaggcta\n+>KT591532.1\n+tatctcgtgtccaaactgatatccttattcacttgatgcaaccccggcagcttgtgttcc\n+gacctgaagtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat\n+actgccgggcccgcgccggccgctgtcttgaggtgggcgctcacccaagatctattaatg\n+ataaccccaatgttctgcaccggtgcttcctccgcccggtcggaagagacgtccagcgtt\n+ggtactctgcccccactcgtggcccagcggctaactgccgccgctctgcgctacgcggtt\n+tgccccctgtcgatcgcacatactgcttcgacgggttttcccgctgcgcttttgccgcag\n+agaccgggattgctctgtactcactgcatgatctttggccctcggacgttgcggaggcta\n+>KT591533.1\n+tatctcgtgtccaaactgatatccttattcacttgatgcaaccccggcagcttgtgttcc\n+gacctgaagtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat\n+actgccgggcccgcgccggccgctgtcttgaggtgggcgctcacccaagatctattaatg\n+ataaccccaatgttctgcaccggtgcttcctccgcccggtcggaagagacgtccagcgtt\n+ggtactctgcccccactcgtggcccagcggctaactgccgccgctctgcgctacgcggtt\n+tgccccctgtcgatcgcacatactgcttcgacgggttttcccgctgcgcttttgccgcag\n+agaccgggattgctctgtactcactgcatgatctttggccctcggacgttgcggaggcta\n' |
| b |
| diff -r 000000000000 -r 462e62be07e1 test-data/test1.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.log Sat Jan 27 12:34:39 2024 +0000 |
| b |
| @@ -0,0 +1,35 @@ +VARVAMP log + +MODE = single + + +ARG SETTINGS + +THRESHOLD = 0.8 +PRIMER_ALLOWED_N_AMB = 3 +AMPLICON_OPT_LENGTH = 300 +AMPLICON_MAX_LENGTH = 400 +REPORT_N_AMPLICONS = 5 + +CONFIG SETTINGS + +PRIMER_TMP = (56, 63, 60) +PRIMER_GC_RANGE = (35, 65, 50) +PRIMER_SIZES = (18, 24, 21) +PRIMER_HAIRPIN = 47 +PRIMER_MAX_POLYX = 4 +PRIMER_MAX_DINUC_REPEATS = 4 +PRIMER_GC_END = (1, 3) +PRIMER_MAX_DIMER_TMP = 47 +PRIMER_MIN_3_WITHOUT_AMB = 3 +PCR_MV_CONC = 100 +PCR_DV_CONC = 2 +PCR_DNTP_CONC = 0.8 +PCR_DNA_CONC = 15 +PRIMER_TM_PENALTY = 2 +PRIMER_GC_PENALTY = 0.2 +PRIMER_SIZE_PENALTY = 0.5 +PRIMER_MAX_BASE_PENALTY = 10 +PRIMER_3_PENALTY = (32, 16, 8, 4, 2) +PRIMER_PERMUTATION_PENALTY = 0.1 + |
| b |
| diff -r 000000000000 -r 462e62be07e1 test-data/test2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.log Sat Jan 27 12:34:39 2024 +0000 |
| b |
| @@ -0,0 +1,37 @@ +VARVAMP log + +MODE = tiled + +WARNING: your amplicon lengths might be to small. Consider increasing +WARNING: your intended overlap is higher than half of your optimal length. This reduces how well varvamps will find overlapping amplicons. Consider decreasing. + +ARG SETTINGS + +THRESHOLD = 0.6 +PRIMER_ALLOWED_N_AMB = 2 +AMPLICON_OPT_LENGTH = 150 +AMPLICON_MAX_LENGTH = 300 +MIN_OVERLAP = 100 + +CONFIG SETTINGS + +PRIMER_TMP = (56, 63, 60) +PRIMER_GC_RANGE = (35, 65, 50) +PRIMER_SIZES = (18, 24, 21) +PRIMER_HAIRPIN = 47 +PRIMER_MAX_POLYX = 4 +PRIMER_MAX_DINUC_REPEATS = 4 +PRIMER_GC_END = (1, 3) +PRIMER_MAX_DIMER_TMP = 47 +PRIMER_MIN_3_WITHOUT_AMB = 3 +PCR_MV_CONC = 100 +PCR_DV_CONC = 2 +PCR_DNTP_CONC = 0.8 +PCR_DNA_CONC = 15 +PRIMER_TM_PENALTY = 2 +PRIMER_GC_PENALTY = 0.2 +PRIMER_SIZE_PENALTY = 0.5 +PRIMER_MAX_BASE_PENALTY = 10 +PRIMER_3_PENALTY = (32, 16, 8, 4, 2) +PRIMER_PERMUTATION_PENALTY = 0.1 + |
| b |
| diff -r 000000000000 -r 462e62be07e1 test-data/test3.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.log Sat Jan 27 12:34:39 2024 +0000 |
| b |
| @@ -0,0 +1,45 @@ +VARVAMP log + +MODE = qpcr + + +ARG SETTINGS + +THRESHOLD = 0.7 +PRIMER_ALLOWED_N_AMB = 1 +PROBE_ALLOWED_N_AMB = 1 +TEST_DELTAG_N_AMPLICONS = 180 +DELTAG_CUTOFF = -15 + +CONFIG SETTINGS + +PRIMER_TMP = (56, 63, 60) +PRIMER_GC_RANGE = (35, 65, 50) +PRIMER_SIZES = (18, 24, 21) +PRIMER_HAIRPIN = 47 +PRIMER_MAX_POLYX = 4 +PRIMER_MAX_DINUC_REPEATS = 4 +PRIMER_GC_END = (1, 3) +PRIMER_MAX_DIMER_TMP = 47 +PRIMER_MIN_3_WITHOUT_AMB = 3 +PCR_MV_CONC = 100 +PCR_DV_CONC = 2 +PCR_DNTP_CONC = 0.8 +PCR_DNA_CONC = 15 +PRIMER_TM_PENALTY = 2 +PRIMER_GC_PENALTY = 0.2 +PRIMER_SIZE_PENALTY = 0.5 +PRIMER_MAX_BASE_PENALTY = 10 +PRIMER_3_PENALTY = (32, 16, 8, 4, 2) +PRIMER_PERMUTATION_PENALTY = 0.1 +QPROBE_TMP = (64, 70, 67) +QPROBE_SIZES = (20, 30, 25) +QPROBE_GC_RANGE = (40, 80, 60) +QPROBE_GC_END = (0, 4) +QPRIMER_DIFF = 2 +QPROBE_TEMP_DIFF = (5, 10) +QPROBE_DISTANCE = (4, 15) +QAMPLICON_LENGTH = (70, 200) +QAMPLICON_GC = (40, 60) +QAMPLICON_DEL_CUTOFF = 4 + |
| b |
| diff -r 000000000000 -r 462e62be07e1 test-data/test4.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test4.log Sat Jan 27 12:34:39 2024 +0000 |
| b |
| @@ -0,0 +1,35 @@ +VARVAMP log + +MODE = single + + +ARG SETTINGS + +THRESHOLD = 0.8 +PRIMER_ALLOWED_N_AMB = 3 +AMPLICON_OPT_LENGTH = 300 +AMPLICON_MAX_LENGTH = 400 +REPORT_N_AMPLICONS = 5 + +CONFIG SETTINGS + +PRIMER_TMP = (56, 63, 60) +PRIMER_GC_RANGE = (20, 80, 50) +PRIMER_SIZES = (18, 24, 21) +PRIMER_HAIRPIN = 47 +PRIMER_MAX_POLYX = 4 +PRIMER_MAX_DINUC_REPEATS = 4 +PRIMER_GC_END = (1, 3) +PRIMER_MAX_DIMER_TMP = 47 +PRIMER_MIN_3_WITHOUT_AMB = 3 +PCR_MV_CONC = 100.0 +PCR_DV_CONC = 2.0 +PCR_DNTP_CONC = 0.8 +PCR_DNA_CONC = 15.0 +PRIMER_TM_PENALTY = 2.0 +PRIMER_GC_PENALTY = 0.2 +PRIMER_SIZE_PENALTY = 0.5 +PRIMER_MAX_BASE_PENALTY = 10 +PRIMER_3_PENALTY = (32, 16, 8, 4, 2) +PRIMER_PERMUTATION_PENALTY = 0.1 + |
| b |
| diff -r 000000000000 -r 462e62be07e1 varvamp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/varvamp.xml Sat Jan 27 12:34:39 2024 +0000 |
| [ |
| b'@@ -0,0 +1,463 @@\n+<tool id="varvamp" name="varVAMP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">\n+ <description>design primers for highly diverse viruses</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <xrefs>\n+ <xref type="bio.tools">varvamp</xref>\n+ </xrefs>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>\n+ </requirements>\n+ <version_command>varvamp --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+VARVAMP_CONFIG=custom_config varvamp\n+\n+$mode.m_select\n+#if $mode.main_params.specify_how in ("set_threshold", "set_both"):\n+ --threshold $mode.main_params.threshold\n+#end if\n+#if $mode.main_params.specify_how in ("set_n_ambig", "set_both"):\n+ --n-ambig $mode.main_params.n_ambig\n+ #if $mode.m_select == "qpcr":\n+ --pn-ambig $mode.main_params.pn_ambig\n+ #end if\n+#end if\n+#if str( $mode.m_select ) == "single":\n+ --opt-length $mode.opt_length\n+ --max-length $mode.max_length\n+ #if $mode.limit_report.choice == "yes":\n+ --report-n $mode.limit_report.report_n\n+ #end if\n+#elif str( $mode.m_select ) == "tiled":\n+ --opt-length $mode.opt_length\n+ --max-length $mode.max_length\n+ --overlap $mode.overlap\n+#elif str( $mode.m_select ) == "qpcr":\n+ --test-n $mode.test_n\n+ --deltaG $mode.deltaG\n+#end if\n+#if $mode.filter_blast_hits.choice == "yes":\n+ --database \'${mode.filter_blast_hits.database.extra_files_path}/blastdb\'\n+#end if\n+--threads \\${GALAXY_SLOTS:-1}\n+\n+\'$alignment\'\n+results/\n+\n+#if $mode.m_select == \'qpcr\' and $mode.scheme_outputs and \'primer_seqs\' in $mode.scheme_outputs:\n+ ## make the primer sequences fasta discoverable under the same name that is used in "single" mode\n+ && mv results/oligos.fasta results/primers.fasta\n+#end if\n+#if $mode.m_select == \'tiled\' and $mode.scheme_outputs and \'primer_dimers\' in $mode.scheme_outputs:\n+ ## ensure the unsolvable_primer_dimers.tsv file, which varVAMP creates only conditionally, exists in all cases, in which we try to discover it as an output\n+ && cp -n dimers_fallback.tsv results/unsolvable_primer_dimers.tsv\n+#end if\n+ ]]></command>\n+ <configfiles>\n+ <configfile filename="custom_config"><![CDATA[#if $mode.advanced_config.customize == "yes":\n+PRIMER_TMP = ($mode.advanced_config.basic_primer_params.PRIMER_TMP_min, $mode.advanced_config.basic_primer_params.PRIMER_TMP_max, $mode.advanced_config.basic_primer_params.PRIMER_TMP_opt)\n+PRIMER_GC_RANGE = ($mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_min, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_max, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_opt)\n+PRIMER_SIZES = ($mode.advanced_config.basic_primer_params.PRIMER_SIZES_min, $mode.advanced_config.basic_primer_params.PRIMER_SIZES_max, $mode.advanced_config.basic_primer_params.PRIMER_SIZES_opt)\n+PRIMER_MAX_POLYX = $mode.advanced_config.basic_primer_params.PRIMER_MAX_POLYX\n+PRIMER_MAX_DINUC_REPEATS = $mode.advanced_config.basic_primer_params.PRIMER_MAX_DINUC_REPEATS\n+PRIMER_HAIRPIN = $mode.advanced_config.basic_primer_params.PRIMER_HAIRPIN\n+PRIMER_GC_END = ($mode.advanced_config.basic_primer_params.PRIMER_GC_END_min, $mode.advanced_config.basic_primer_params.PRIMER_GC_END_max)\n+PRIMER_MIN_3_WITHOUT_AMB = $mode.advanced_config.basic_primer_params.PRIMER_MIN_3_WITHOUT_AMB\n+PRIMER_MAX_DIMER_TMP = $mode.advanced_config.basic_primer_params.PRIMER_MAX_DIMER_TMP\n+ #if str($mode.m_select) == "qpcr":\n+QPROBE_TMP = ($mode.advanced_config.qpcr_params.QPROBE_TMP_min, $mode.advanced_config.qpcr_params.QPROBE_TMP_max, $mode.advanced_config.qpcr_params.QPROBE_TMP_opt)\n+QPROBE_SIZES = ($mode.advanced_config.qpcr_params.QPROBE_SIZES_min, $mode.advanced_config.qpcr_params.QPROBE_SIZES_max, $mode.advanced_config.qpcr_params.QPROBE_SIZES_opt)\n+QPROBE_GC_RANGE = ($mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_min, $mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_max, $mode.advanced_con'..b' <conditional name="main_params">\n+ <param name="specify_how" value="set_both"/>\n+ <param name="threshold" value="0.8"/>\n+ <param name="n_ambig" value="3"/>\n+ </conditional>\n+ <param name="opt_length" value="300"/>\n+ <param name="max_length" value="400"/>\n+ <conditional name="limit_report">\n+ <param name="choice" value="yes" />\n+ <param name="report_n" value="5"/>\n+ </conditional>\n+ <conditional name="advanced_config">\n+ <param name="customize" value="yes"/>\n+ <section name="basic_primer_params">\n+ <param name="PRIMER_GC_RANGE_min" value="20"/>\n+ <param name="PRIMER_GC_RANGE_max" value="80"/>\n+ </section>\n+ </conditional>\n+ <param name="scheme_outputs" value=""/>\n+ <param name="aln_cons_outputs" value=""/>\n+ <param name="plot_outputs" value=""/>\n+ <param name="misc_outputs" value=""/>\n+ </conditional>\n+ <output name="varvamp_log" ftype="txt" compare="contains" file="test4.log" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**What it does**\n+\n+variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.\n+\n+For a lot of virus genera it is difficult to design pan-specific primers. varVAMP solves this by introducing ambiguous characters into primers and minimizes mismatches at the 3\' end. Primers might not work for some sequences of your input alignment but should recognize the large majority.\n+\n+varVAMP can be run in three different **modes**:\n+\n+* SINGLE: varVAMP searches for the very best primers and reports back non-overlapping amplicons which can be used for PCR-based screening approaches.\n+* TILED: varVAMP uses a graph based approach to design overlapping (tiled) amplicons that together cover the entire viral genome. This designs amplicons that are suitable for Oxford Nanopore or Illumina based full-genome sequencing.\n+* QPCR: varVAMP searches for small amplicons with an optimized internal probe (TaqMan). It minimizes temperature differences between the primers and checks for amplicon secondary structures.\n+\n+Algorithmic parameters:\n+\n+These are explained very well on the `How varVAMP works <https://github.com/jonas-fuchs/varVAMP/blob/master/docs/how_varvamp_works.md>`__ page of the varVAMP documentation.\n+\n+Outputs:\n+\n+This tool can produce lots of informative output and the different modes come with what we hope are reasonable default choices.\n+\n+The most important output, however, is the **Analysis Log**, which will always be generated and contains essential information about what parameters where used by varVAMP during the run and about intermediate results. You should always check this file. Together with the tool\'s standard output and error streams, it is the place to spot issues with your analysis and to start debugging them.\n+\n+.. class:: infomark\n+\n+Testing with a new alignment/analysis:\n+\n+As a first check whether a new alignment of viral sequences can be used with specific settings of the tool, it may help to disable all configurable outputs, which will leave you with only the Analysis Log. This will be enough to see if there are any errors with the combination of alignment and settings, and whether you are on a roughly correct track (varVAMP reports some primers, for example). This way, you\'re not flooding your analysis history with lots of likely useless datasets, and once you\'ve fixed potential issues you can add back more outputs and rerun the analysis.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">https://github.com/jonas-fuchs/varVAMP/</citation>\n+ </citations>\n+</tool>\n' |