# HG changeset patch
# User iuc
# Date 1706358879 0
# Node ID 462e62be07e17b6417ffd35bd7e1685910682748

planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 7f509fd29e994d1561ff9de14f26cf49f018dd2d

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
@@ -0,0 +1,138 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">1.1.1</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>
+                <option value="set_both">Specify values for both</option>
+            </param>
+            <when value="set_n_ambig">
+                <param argument="--n-ambig" type="integer" min="0" value="2" label="Maximum number of ambiguous nucleotides per primer to be tolerated (default: 2)" />
+                <yield />
+            </when>
+            <when value="set_threshold">
+                <param argument="--threshold" type="float" min="0.0" max="1.0" value="0.8" label="Threshold for consensus nucleotides" />
+            </when>
+            <when value="set_both">
+                <param argument="--threshold" type="float" min="0.0" max="1.0" value="0.8" label="Threshold for consensus nucleotides" />
+                <param argument="--n-ambig" type="integer" min="0" value="2" label="Maximum number of ambiguous nucleotides per primer to be tolerated" />
+                <yield />
+            </when>
+        </conditional>
+    </xml>
+    <xml name="amplicon_length_restrictions">
+        <param argument="--opt-length" type="integer" min="1" value="1000" label="Optimal length of the amplicons" />
+        <param argument="--max-length" type="integer" min="1" value="1500" label="Maximal length of the amplicons" />
+    </xml>
+    <xml name="blast_options">
+        <conditional name="filter_blast_hits">
+            <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." >
+                    <option value="no">No, don't consider off-target products</option>
+                    <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param argument="--database" type="data" format="blastdbn" label="BLAST database" />
+                <conditional name="blast_advanced_cond">
+                    <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." >
+                        <option value="no">No, use varVAMP default settings</option>
+                        <option value="yes">Yes</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <section name="blast_params" title="BLAST parameters">
+                            <param name="evalue" type="integer" min="0" value="5000" label="BLAST expect (E) value"/>
+                            <param name="reward" type="integer" min="0" value="1" label="BLAST reward (for a nucleotide match)"/>
+                            <param name="penalty" type="integer" max="0" value="-1" label="BLAST penalty (for a mismatch)"/>
+                            <param name="gapopen" type="integer" min="0" value="2" label="BLAST gapopen" help="Cost to open a gap"/>
+                            <param name="gapextend" type="integer" min="0" value="1" label="BLAST gapextend" help="Cost to extend a gap"/>
+                        </section>
+                        <section name="blast_hits_usage" title="varVAMP settings for handling BLAST hits">
+                            <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" />
+                            <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" />
+                            <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." />
+                        </section>
+                    </when>
+                </conditional>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="customize_advanced">
+        <conditional name="advanced_config">
+            <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.">
+                <option value="no">No, use defaults for advanced settings</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <section name="basic_primer_params" title="Constraints on amplicon primers" expanded="false">
+                    <param name="PRIMER_TMP_min" type="integer" min="0" value="56" label="Minimal melting temperature"/>
+                    <param name="PRIMER_TMP_max" type="integer" min="0" value="63" label="Maximal melting temperature"/>
+                    <param name="PRIMER_TMP_opt" type="integer" min="0" value="60" label="Optimal melting temperature"/>
+                    <param name="PRIMER_GC_RANGE_min" type="integer" min="0" max="100" value="35" label="Minimal GC-content" />
+                    <param name="PRIMER_GC_RANGE_max" type="integer" min="0" max="100" value="65" label="Maximal GC-content" />
+                    <param name="PRIMER_GC_RANGE_opt" type="integer" min="0" max="100" value="50" label="Optimal GC-content" />
+                    <param name="PRIMER_SIZES_min" type="integer" min="1" value="18" label="Minimal primer size" />
+                    <param name="PRIMER_SIZES_max" type="integer" min="1" value="24" label="Maximal primer size" />
+                    <param name="PRIMER_SIZES_opt" type="integer" min="1" value="21" label="Optimal primer size" />
+                    <param name="PRIMER_MAX_POLYX" type="integer" min="1" value="4" label="Maximal length of polyX runs in primer" />
+                    <param name="PRIMER_MAX_DINUC_REPEATS" type="integer" min="0" value="4" label="Maximal length of dinucleotide repeats in primer" />
+                    <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" />
+                    <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" />
+                    <param name="PRIMER_MIN_3_WITHOUT_AMB" type="integer" min="0" value="3" label="Minimal length of 3'-end without ambiguous bases." />
+                    <param name="PRIMER_HAIRPIN" type="integer" min="0" value="47" label="Maximal melting temperature for secondary structures (hairpins) in primer" />
+                    <param name="PRIMER_MAX_DIMER_TMP" type="integer" min="0" value="47" label="Maximal melting temperature for primer dimers (homo- or heterodimers)" />
+                </section>
+                <yield />
+                <section name="pcr_params" title="PCR Parameters" expanded="false">
+                    <param name="PCR_MV_CONC" type="float" min="0" value="100" label="Monovalent cations mM conc." />
+                    <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>
+                    </param>
+                    <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." />
+                </section>
+            </when>
+        </conditional>
+    </xml>
+    <xml name="primer_scheme_outputs">
+        <param name="scheme_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Primer scheme outputs">
+            <option value="primer_seqs" selected="true">Sequences of all designed oligos</option>
+            <option value="primer_binding_sites" selected="true">Primer binding sites in BED format; includes primer penalties (lower is better) as the score column</option>
+            <option value="amplicon_sites" selected="true">Amplicon locations in BED format; includes amplicon penalties (lower is better) in the score column</option>
+            <option value="primer_details" selected="true">Primer details in tabular format</option>
+            <yield />
+        </param>
+    </xml>
+    <xml name="consensus_outputs">
+        <param name="aln_cons_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Consensus sequence and alignment-related outputs">
+            <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>
+            <option value="majority_consensus">Consensus sequence without ambiguous nucleotide codes, but with the most prevalent nucleotide at each position instead.</option>
+            <option value="alignment_cleaned">The preprocessed alignment used to build consensus sequences</option>
+        </param>
+    </xml>
+    <xml name="graphical_outputs">
+        <param name="plot_outputs" type="select" display="checkboxes" multiple="true" optional="true" label="Graphical outputs">
+            <option value="amplicon_plot" selected="true">Amplicon design overview</option>
+            <option value="per_base_mismatches" selected="true">Per-primer barplot of mismatches to input sequences</option>
+        </param>
+    </xml>
+    <xml name="miscellaneous_outputs">
+        <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.">
+            <option value="primer_regions">List of all candidate regions of the consensus sequence that were evaluated for primers in BED format</option>
+            <yield />
+        </param>
+    </xml>
+</macros>
+
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
@@ -0,0 +1,2 @@
+>ambiguous_consensus
+tatcccgtrtycaractgayatccttattaayytgatgcaaccycgrcagcttgtkttccgrccygaagtyytstggaaycayccgatccagcgrgtyatacataatgagctggagcartactgccgwgcycgygctggycgytgyctkgargtkggsgcycayccaagatcyatyaatgayaacccyaatgtyytgcaccggtgcttyctycgcccggtyggdagagaygtmcagcgytggtaytcygccccsacycgyggyccagcggcyaaytgccgccgytcygcgctacgyggyytgccccctgtcgaycgyacmtaytgcttcgacgggttytcccgctgcgcytttgccgctgagacyggratygctttataytcactrcatgacctytggccytcggaygtygcggaggcya
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
@@ -0,0 +1,1104 @@
+>MF444058.1
+tatctcgtgttcaaactgagatccttattaacctgatgcaaccccggcagctcgtgtttc
+ggcctgaagtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat
+actgccgagcccgcgctggccgttgtcttgaggtgggcgctcacccaagatctattaatg
+acaaccccaatgtcctacaccggtgctttctccgcccggttgggagagacgtccagcgct
+ggtattccgcccccacccgtggtccagcggccaattgccgccgctctgcgctacgcggct
+tgccccctgtcgatcgtacatattgcttcgatgggttttcccgctgcgcctttgccgccg
+agaccgggatcgctttatactcactgcatgacctttggccctcggacgttgcggaggcta
+>MN646693.1
+tatctcgtattcagactgatatccttattaacctgatgcaacctcggcagcttgttttcc
+ggcctgaagttctctggaatcacccgatccagcgagttatacataatgagctggagcaat
+actgccgagcccgcgctggccgctgccttgaggtgggcgctcacccaagatccatcaatg
+ataaccccaatgttctgcaccggtgctttctccgcccggttggcagagacgtccagcgct
+ggtactccgcccccactcgtggtccagcggctaactgccgccgctctgcgctacgtggtt
+tgccccctgtcgatcgtacatattgctttgacgggttctcccgctgcgcctttgccgctg
+agaccgggattgctttatactcactgcacgacctttggccctcggacgttgcggaggcca
+>KT591534.1
+tatctcgtgtccaaactgatatccttattcacttgatgcaacctcggcagcttgtgttcc
+gacctgaagtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat
+actgccgggcccgcgccggccgctgtcttgaggtgggcgctcacccaagatctattaatg
+ataaccccaatgttctgcaccggtgcttcctccgcccggtcggaagagacgtccagcgtt
+ggtactctgcccccactcgtggcccagcggctaactgccgccgctctgcgctacgtggtt
+tgccccctgtcgatcgcacatactgcttcgacgggttttcccgctgcgcttttgccgcag
+agaccgggattgctctgtactcactgcatgatctttggccctcggacgttgcggaggcta
+>KC166971.1
+tatcccgtgttcaaactgatatccttatyaacttgatgcaacctcgacagcttgtgttcc
+ggcccgaagtcctctggaatcatccgatccagcgagttatacataatgagctggagcaat
+actgccgrgcccgcgctggccgttgtcttgaagtgggygcccacccaagatctattaatg
+ataaccccaatgttytgcaccggtgctttctccgcccggttggaagagacgtccagcgct
+ggtattcygcccccactcgyggtccagcggctaattgccgccgttctgcgctacgcggtt
+tgccccctgtcgaccgcacgtattgcttcgacgggttctcccgctgcgcctttgccgctg
+agaccgggattgctttatactcactgcatgacctttggccttcggatgtcgcggaggcta
+>MF444034.1
+tatcccgtgttcaaactgaaatccttattaacctgatgcaacctcgacagcttgtgttcc
+ggcccgaagtcctctggaatcatccgatccagcgagttatacacaatgagctggagcaat
+actgccgagcccgcgctggccgttgtcttgaagtgggcgcccatccaagatctattaatg
+ataaccccaatgttctgcaccggtgctttctccgcccggttggtagagacgtccagcgct
+ggtattccgcccccactcgtggcccagcggctaattgccgccgttctgcgttacgcggct
+tgccccctgtcgaccgcacatattgcttcgacgggttctcccgctgcgcctttgccgctg
+agaccgggatcgctttatactcactgcatgacctttggccttcggatgttgcggaggcta
+>MF444119.1
+tatcccgtgtccaaactgatatccttattaacttgatgcaacctcgacagcttgtgttcc
+ggcccgaagtcttctggaatcatccgatccagcgagttatacataatgagctggagcagt
+actgccgagcccgcgctggccgttgtcttgaagtgggcgcccacccaagatctattaatg
+ataaccccaatgttctgcaccggtgctttcttcgcccggttggaagagacgtccagcgct
+ggtactccgcccccactcgtggcccagcggctaattgccgccgttccgcgctacgcggct
+taccccctgtcgaccgcacatattgcttcgacgggttttcccgctgcgcctttgccgctg
+agaccgggatcgctttatactcactgcatgacctttggccttcggatgtcgcggaggcta
+>MF444054.1
+tatcccgtatccagactgatatcctcattaacctgatgcaaccccggcagcttgttttcc
+ggcctgaagttctctggaatcacccgatccagcgggttatacataatgagttggagcaat
+actgccgagcccgcgctggccgctgtcttgaggtgggcgctcacccaagatccatcaatg
+ataaccccaatgttctgcaccggtgctttctccgcccggtcggtagagacgtccagcgct
+ggtattctgcccccactcgtggcccggcggctaactgccgtcgctctgcgctacgtggtt
+tgccccctgtcgatcgtacatactgcttcgacgggttttcccgctgtgcttttgctgctg
+agaccgggattgctttatactcactgcatgacctttggccctcggacgttgcggaggcca
+>MN646691.1
+tatcccgtgcccagactgatatccttataaacctgatgcaaccccggcagctcgtgtttc
+gtcccgaagttttgtggaaccacccgatccagcgagtcatacacaatgagctggaacagt
+attgccgtgctcgtgctggtcgctgtctggaggtgggggctcatccaagatctattaatg
+acaatcctaatgtcctgcatcggtgctttcttcgcccggttgggagagacgtacagcgct
+ggtactctgccccgactcgcggtccagcggctaactgccgccgctctgcgttacgtggcc
+tgccccctgtcgatcgtacctactgcttcgacgggttttcccgttgcgcatttgccgctg
+agactggaattgccctgtactcattacatgacctctggcccgcggatgtcgcggaagcca
+>MN646690.1
+tatcccgtgcccagactgatatccttataaacctgatgcaaccccggcagctcgtgtttc
+gtcccgaagttttgtggaaccacccgatccagcgagtcatacacaatgagctggaacagt
+attgccgtgctcgtgctggtcgctgtctggaggtgggggctcatccaagatctattaatg
+acaatcctaatgtcctgcatcggtgctttcttcgcccggttgggagagacgtacagcgct
+ggtactctgccccgactcgcggtccagcggctaactgccgccgctctgcgttacgtggcc
+tgccccctgtcgatcgtacctactgcttcgacgggttttcccgttgcgcatttgccgctg
+agactggaattgccctgtactcattacatgacctctggcccgcggatgtcgcggaagcca
+>MN646695.1
+tatcccgtactcagactgatatccttattaacctgatgcaaccccggcagcttgtttttc
+ggcctgaagttctctggaatcacccgatccagcgggttatacataatgagctggagcaat
+actgccgagcccgcgctggccgctgtcttgaggtgggcgctcacccaagatccatcaatg
+ataaccccaatgttctgcaccggtgcttccttcgcccggtcggtagagacgtccagcgct
+ggtattctgcccctactcgtggcccagcggctaactgccgccgctctgcgctacgtggtt
+tgccccctgtcgatcgtacatactgcttcgacgggttctcccgctgcgcctttgccgctg
+agaccggaattgctttatactcactgcatgacctttggccctcggacgttgcggaggcca
+>MF444088.1
+tatctcgtgttcaaactgatatccttattaacctgatgcaaccccgacagcttgtgttcc
+ggcctgaggtcctctggaatcacccgatccaacgagtcatacataatgaactggagcaat
+actgccgagcccgtgccggtcgctgtcttgaggttggcgctcacccaagatctattaatg
+ataaccccaatgttttgcaccggtgctttctccgcccggttgggagagatgtccagcgtt
+ggtactccgctcccactcgtggtccagcggctaattgccgtcgttctgcgctccgcggtt
+taccccctgtcgatcgcacatattgcttcgacgggttctcccgctgcgcttttgccgctg
+agaccgggatcgctctatactcactgcacgacctctggccttcggatgtcgcggaggcca
+>AB850879.1
+tatcccgtattcagactgatatccttattaacctgatgcaaccccggcagcttgttttcc
+ggcctgaagttctctggaatcacccgatccagcgggttatccataatgagctggagcaat
+actgccgagctcgcgctggccgctgtcttgaggtgggcgctcacccgagatccatcaatg
+ataaccccaatgttctgcaccggtgctttcttcgcccggtcggtagagacgtccagcgct
+ggtattctgcccccactcgtggtccagcggctaactgccgccgctctgcactacgtggtt
+tgccccctgtcgatcgtacatattgcttcgacgggttttcccgctgcgcctttgccgctg
+agaccggaattgctttatattcactgcatgacctttggccctcggacgtcgcggaggcca
+>MF444138.1
+tatcccgtgttcaaactgatatccttattaatttgatgcaacctcgacagcttgtgttcc
+ggcctgaagtcctctggaatcatccgatccagcgagttatacataatgagctggagcagt
+actgccgagcccgcgctggccgttgtcttgaagtgggcgctcacccaagatctattaatg
+ataaccccaatgttctgcaccggtgctttctccgcccggttgggagagacgtccagcgct
+ggtattccgcccccactcgtggcccagcggctaactgccgccgttctgcgctacgcggct
+tgccccctgtcgaccgcacgtactgcttcgacgggttctcccgctgcgcctttgccgctg
+agactgggatcgctttatattcattgcatgacctttggccctcggacgttgcggaggcta
+>MF444123.1
+tatcccgtactcagactgacatccttattaacctgatgcaaccccggcagcttgtcttcc
+ggcctgaagttctctggaatcatccgatccaacgggttatacataatgagctggagcaat
+actgccgagctcgcgctggccgctgtcttgaggtgggcgctcacccaagatccattaacg
+ataaccccaatgttctgcaccggtgtttcctccgcccggtcgggagggatgtccagcgct
+ggtattccgccccnacccgcgggccagcggctaactgccgccgctctgcgctacgtggtt
+tgccccntgtcgatcgcacatattgcttcgacgggttctcccgctgcgcctttgccgccg
+agaccgggattgctttatactcactgcatgacctctggccctcggacgttgcggaggcca
+>EU495148.1
+tatctcgtgttcaaactgagatccttattaacctgatgcaaccccgacagcttgtgtttc
+ggcctgaggtcctctggaaccatccgatccagcgagtcatacacaacgagctggagcagt
+actgccgagcccgcgctggccgttgtcttgaggtgggcgctcacccaagatccattaatg
+acaaccccaatgtcctacaccggtgctttctccgcccggttggaagagacgtccagcgct
+ggtactccgcccccacccgtggtccagcggccaattgtcgccgctctgcgctacgcggcc
+tgccccctgtcgatcgcacatattgttttgatgggttttcccgctgcgcctttgccgctg
+agaccggggtcgctttatactcactgcatgacctttggccctcggacgttgcggaggcta
+>MF444027.1
+tatcccgtgttcaaactgaaatccttattaacctgatgcaacctcgacagcttgtgttcc
+ggcccgaagtcctctggaatcatccgatccagcgagttatacacaatgagctggagcaat
+actgccgagcccgcgctggccgttgtcttgaagtgggcgcccatccaagatctattaatg
+ataaccccaatgttctgcaccggtgctttctccgcccggttggtagagacgtccagcgct
+ggtattccgcccccactcgtggcccagcggctaattgccgccgttctgcgttacgcggct
+tgccccctgtcgaccgcacatattgcttcgacgggttctcccgctgcgcctttgccgctg
+agaccgggatcgctttatactcactgcatgacctttggccttcggatgttgcggaggcta
+>MF444055.1
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+agaccgggattgctctatattcactgcatgacctctggccttcggacgttgcggaggcca
+>MF444101.1
+tatcccgtgttcaaactgacatccttataaacctgatgcaaccccggcagcttgtatttc
+ggcctgaagtcctctggaatcacccgatccagcgagttatacataacgagctggagcaat
+actgccgagcccgcgctggtcgttgccttgaggtgggcgctcacccaaggtctattaatg
+acaacccmaatgttctgcaccggtgctttctccgcccggttgggagagacgtccaacgct
+ggtactctgcccccacccgtggtccagcggctaattgccgccgttctgcgctacgcggtt
+tgccccctgtcgatcgcacatactgctttgacgggttctcccgctgcgcctttgccgctg
+agaccggtatcgctttatactcactgcatgatctttggccctcggatgttgctgaggcta
+>MF444135.1
+tatcccgtgttcaaactgatatcctcataaacttaatgcaaccccggcagctcgtgttcc
+gccctgaagtcctctggaaccatccgatccagcgggtcatacataacgagctggagcaat
+actgccgagcccgcgctggccgatgcctcgaggtgggtgcccatccaaggtccattaatg
+acaaccctaatgttctgcaccggtgcttcctccgcccagttgggagagatgtccagcgct
+ggtactcagcccctactcgtggcccagcagccaattgtcgccgttcagcgctacgtggtt
+tgcctcctgtcgatcgcacatactgcttcgacgggttctcccgctgcgcttttgctgctg
+agaccgggattgctttatactcactacatgacctttggccctcggacgttgcggaggcta
+>MF444091.1
+tatcccgtgttcagaccgatatccttattaatctgatgcaacctcggcagctcgttttcc
+ggcctgaagtcttctggaatcatccaattcagcgagtcatacataatgagttggagcaat
+actgccgggcccgtgccggccgctgcctagaagtaggcgctcacccgaggtccatcaatg
+acaatcctaatgtcctgcaccggtgctttcttcgcccggtcggcagagatgttcagcgct
+ggtattctgctcctactcgtggtccggcggccaattgccgtcgttctgcgcttcgcggtc
+tgccccccgttgatcgcacttactgtttcgacgggttttcccgctgcgcttttgccgccg
+agaccgggattgctttatactcactacatgacctctggccttcggacgttgcggaggcca
+>MF444126.1
+tatcccgtgttcaaactgatatccttattaacctgatgcaacctcgacagcttgtattcc
+ggcctgaagtcctctggaaccatccgatccagcgagtcatacataatgagttggagcaat
+actgccgtgcccgcgctggtcgctgtcttgaggtgggcgctcacccaagatctattaatg
+acaaccctaatgttctgcaccggtgcttcctccgcccggttgggagggacgtccagcgct
+ggtattctgctcccactcgtggtccagcggctaactgtcgccgttctgcgctacgtggtc
+tgcctcccgtcgatcgcacatattgcttcgacgggttctcccgctgcgcctttgccgctg
+agaccgggatcgctttatattcactgcatgacctttggccttcggatgtcgccgaggcta
+>LC406633.1
+tatcccgtgttcagactgacatccttattaatctgatgcaaccccggcagcttgtattcc
+ggcctgaagtcttttggaaccacccgattcagcgagtcatacataacgaattggagcagt
+actgccgggcccgcgctggtcgttgccttgaagttggcgcccatccgagatccatcaatg
+acaatcttaatgttctgcaccggtgctttcttcgcccggttggcagagatgtccagcgtt
+ggtattctgcccccacccgtggtccggcggctaactgccgccgttctgctcttcgcggct
+tgccccctgtcgatcgtacatactgcttcgatgggttctcccgttgtgcttttgccgctg
+aaaccgggattgctttatattcactgcatgacctctggccttcggatgttgcggaggcca
+>MF444032.1
+tatctcgtgttcaaactgatattcttattaacctgatgcaaccccggcagcttgtgttcc
+gacccgaagtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat
+actgccgagcccgcgctggccgctgtcttgaggtgggcgctcacccgagatccattaacg
+ataaccccaatgtyctgcaccggtgctttcttcgtccggttggaagagacgtccagcgtt
+ggtactctgcccccacccgtggtccagcggctaactgccgccgttctgcgctgcgtggtt
+tgccccctgtcgaccgcacatactgtttcgacgggttctcccgytgcacctttgccgctg
+agaccgggatcgctttatactcattacatgacctttggccctcggatgttgcggaggcta
+>MF444113.1
+tgtcccgcgtccaaactgacatccttatcaacctgatgcaaccccggcagcttgtgttcc
+gacctgaggtcctttggaaccacccaatccagcgagttatacataatgagttggagcaat
+actgccgagcccgcgctggtcgctgccttgaggtgggcgctcacccgaggtctatcaatg
+ataaccctaatgttctgcaccggtgcttcctccgcccggttggaagagacgtccagcgct
+ggtattctgctcccactcgtggaccagcggctaactgccgccgttccgcgcttcgcggtt
+tgccccctgtcgatcgcacatactgcttcgatggattctcccgctgcgcttttgccgctg
+agaccgggattgctttatactcactgcatgacctctggccttcggacgttgcggaggcta
+>MF444109.1
+tgtcccgtactcagactgacatccttattaatttgatgcaaccccggcagctcgtattcc
+gccctgaagttttgtggaatcacccgatccagcgagtcatacacaacgaactggagcaat
+actgccgagctcgcgccggtcgctgtctggaagtaggggctcatccaagatctattaatg
+acaaccccaatgttttacaccggtgcttccttcgcccggttgggagagatgtgcagcgtt
+ggtactccgccccgacccgcggcccagcggctaattgccgccgttctgcactacgcggcc
+taccccctgtcgaccgtacctactgcttcgacgggttttcccgctgtgccttcgctgctg
+agactggaattgctttatactcattacatgacctttggcctgctgatgttgcggaagcca
+>MF444052.1
+tgtcccgtgttcaaactgagattcttattaacctgatgcaaccccggcagcttgttttcc
+gacctgaagtcttctggaaccacccgattcagcgagtcatacataatgagctggaacaat
+actgccgagcccgcgccggtcgttgtcttgaggtgggtgctcacccaagrtccattaatg
+ataaccctaatgttctgcaccggtgctttcttcgcccggttggaagagatgtccagcgct
+ggtactctgctcccactcgtggtccagcggccaaytgtcgccgttctgcgttgcgcggtc
+tgccccctgccgatcgcacgtactgcttcgacgggttctcccgctgcgcctttgccgctg
+agaccgggatcgctttatactcactgcatgacctttggccctcggacgttgcggaggcta
+>MF444046.1
+tatcccgtgttcagactgacatccttattaacttgatgcaaccccggcagcttgtattcc
+ggcctgaagtcctctggaatcacccgatccagcgagttatacataacgagctggagcaat
+actgccgagcccgcgctggtcgttgccttgaggtgggcgctcacccaaggtctattaatg
+acaaccccaatgttctgcaccggtgctttctccgcccggttgggagagacgtccaacgct
+ggtactctgcccccactcgtggtccagcggctaactgccgccgttctgcgctacgcggtc
+tgcctcctgtcgatcgcacatactgctttgacgggttctcccgctgcgcctttgccgctg
+agaccggtatcgctttatactcactgcatgatctttggccctcggatgttgctgaggcta
+>MF444116.1
+tgtcccgtgtccagactgagatccttattaatctgatgcaaccccggcagcttgtgttcc
+gacctgaagtcctctggaaccatccgattcagcgagtcatacataatgagctggagcaat
+actgccgagcccgcgctggccgctgtcttgaggtcggtgcccacccaagatctatcaatg
+ataaccccaacgttctgcaccggtgctttctccgcccggtcggtagagacgtccagcgct
+ggtattctgcccctactcgcggtccagcggccaattgccgccgttctgcgctacgcggtc
+tgccccctgtcgatcgcacatactgcttcgacgggttttcccgctgcgcttttgccgctg
+agaccgggatygccttatactcactgcatgacctttggccctcrgatgttgcggaagcta
+>MF444141.1
+tgtcccgtactcagactgacatccttattaatttgatgcaaccccggcagctcgtattcc
+gccctgaagttttgtggaatcacccgatccagcgagtcatacacaacgaactggagcaat
+actgccgagctcgcgccggtcgctgtctggaagtaggggctcatccaagatctattaatg
+acaaccccaatgttttacaccggtgcttccttcgcccggttgggagagatgtgcagcgtt
+ggtactccgccccgacccgcggcccagcggctaattgccgccgttctgcactacgcggcc
+taccccctgtcgaccgtacctactgcttcgacgggttttcccgctgtgccttcgctgctg
+agactggaattgctttatactcattacatgacctttggcctgctgatgttgcggaagcca
+>MF444104.1
+tatcccgtgtccaaactgatatccttattaacttgatgcaaccccggcaacttgttttcc
+gacctgaagtcctctggaaccatccgatccagcgagttatacataatgagctggagcagt
+actgccgagcccgagctggtcgctgccttgaggtgggcgctcacccaagatccatcaatg
+ataatcccaacgttctgcaccggtgctttctccgtccggttggaagagacgtccagcgct
+ggtattctgcccccactcgtggcccagcggccaactgccgccgttccgcgctacgtggcc
+tgccccctgtcgatcgcacatactgtttcgacgggttttcccgttgcgcctttgctgctg
+agaccgggatcgctttatactcactgcacgatctttggccctcggacgtcgcggaggcta
+>MF444067.1
+tatcccgtgttcaaactgacatccttatcaacttgatgcaaccccggcagcttgtttttc
+gacctgaagttctctggaaccatccgatccagcgagttatacataacgagctggagcagt
+actgccgagctcgtgctggtcgctgccttgaggtgggcgcccacccacgatccattaatg
+ataaccccaatgttttgcaccggtgctttctccgcccggttggaagagatgtccagcgct
+ggtactctgcccctactcgtggtccagcggccaactgccgccgttccgcgttacgtggcc
+tgccccctgtcgatcgcacatactgtttcgacgggttttcccgctgcacctttgctgctg
+agaccggaatcgctttatactcactgcatgatctatggccatcggacgttgcagaggcta
+>MF444080.1
+tatcccgtgtgcaaactgacatccttattaacctgatgcaaccccggcagctcgtgtttc
+ggcctgaagttttctggaaccacccgatccagcgggtcatacataacgagctagagcaat
+actgccgagctcgcgctggccgctgccttgaggtgggtgctcacccgaggtccattaatg
+ataatcctaatgtcctgcaccggtgcttccttcgtccagtcgggagagatgtccagcgtt
+ggtattctgcccccactcgcggcccagcggctaactgccgtcgctccgcactacgtggtt
+tgcctcctgtcgaccgcacatactgcttcgacgggttctcccgctgtgctttcgccgctg
+agaccggaatcgccttatattcactgcatgacctctggccttcggacgttgcggaggcca
+>MF444053.1
+tatcccgtgttcagaccgatatccttattaatctgatgcaacctcggcagctcgttttcc
+ggcctgaagtcttctggaaccatccaattcagcgagtcatacataatgagttggagcaat
+actgccgggcccgtgccggccgctgcctagaagtaggcgctcacccgaggtccatcaatg
+acaatcctaatgtcctgcaccggtgctttcttcgcccggttggcagagatgttcagcgct
+ggtattctgctcctactcgtggtccggcggccaattgccgtcgttctgcgctccgcggtc
+taccccccgttgatcgcacttactgtttcgacgggttttcccgctgcgcttttgccgccg
+agaccgggattgctttatactcactacatgacctctggccttcggacgttgcggaggcca
+>MF444144.1
+tatcccgtgttcaaactgacatccttattaacctgatgcaaccccggcagcttgtgttcc
+gacctgaggtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat
+actgccgagcccgcgctggccgctgccttgaggtgggcgctcacccgaggtctatcaatg
+ataaccctaatgtcctgcaccggtgcttccttcgcccggttggaagagacgtccagcgct
+ggtattctgcccctacccgtggaccagcggccaactgccgccgttctgcgcttcgcggtt
+tgccccctgtcgatcgcacatactgcttcgatgggttctctcgctgcgctttcgccgctg
+agaccgggattgctttatactcactgcatgacctctggccttcggacgttgcggaggcca
+>KF922359.1
+tgtcccgtgttcagaccgatattcttatcaatttgatgcaaccccggcagcttgtatttc
+gccctgaagttctgtggaaccatccgattcagcgagttatacataatgagctagagcagt
+attgccgtgctcgtgctggccgctgcctggaggtcggggctcatccaagatctattaatg
+acaaccctaatgttttgcaccggtgcttcctccgtccggtcgggagggatgtccagcgct
+ggtacactgcaccgactcgcggcccggcggctaactgccgccgctccgcgttacgtggcc
+taccccctgtcgatcgtacctactgtttcgacgggttttcccgctgcgcctttgccgccg
+agactggaattgccttatattcactacatgacctctggcctgcggatgttgcagaggcca
+>MF444062.1
+tatcccgtgtccagactgatatccttattaacttgatgcaaccccggcagcttgtgttcc
+gacctgaagttctctggaaccatccaatccagcgagtgatacataatgaactggagcaat
+actgccgagcccgtgctggccgttgtcttgaggtgggcgcccacccaagatccatcaacg
+ataaccctaatgttctgcatcggtgctttctccgcccggttggaagagacgtccagcgct
+ggtactctgcccccacccgtggtccagcggccaactgccgccgttctgcgctgcgtggtt
+tgcctcctgtcgatcgcacatactgcttcgacgggttttcccgctgcgcctttgcagctg
+agaccgggatcgctttatactcgctgcatgatctttggccctcggacgttgcggaggcta
+>MF444118.1
+tatcccgtgtccagactgacatccttattaatctgatgcaaccccggcagcttgtgttcc
+gacctgaagtcctctggaaccatccgattcagcgagtcatacataatgagctggagcaat
+actgccgagcccgcgctggccgctgtcttgaggtgggcgcccacccaagatctattaatg
+ataaccccaacgttctgcaccggtgctttctccgcccggtcgggagagacgtccagcgct
+ggtattctgcccctactcgcggtccagcggccaattgccgccgttctgcgctacgcggtt
+tgccccctgtcgaccgcacatactgcttcgacgggttttcccgctgcgctttcgccgctg
+agaccgggatcgccttatactcgctgcatgacctttggccctcggacgttgcggaggcta
+>KT591532.1
+tatctcgtgtccaaactgatatccttattcacttgatgcaaccccggcagcttgtgttcc
+gacctgaagtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat
+actgccgggcccgcgccggccgctgtcttgaggtgggcgctcacccaagatctattaatg
+ataaccccaatgttctgcaccggtgcttcctccgcccggtcggaagagacgtccagcgtt
+ggtactctgcccccactcgtggcccagcggctaactgccgccgctctgcgctacgcggtt
+tgccccctgtcgatcgcacatactgcttcgacgggttttcccgctgcgcttttgccgcag
+agaccgggattgctctgtactcactgcatgatctttggccctcggacgttgcggaggcta
+>KT591533.1
+tatctcgtgtccaaactgatatccttattcacttgatgcaaccccggcagcttgtgttcc
+gacctgaagtcctctggaaccacccgatccagcgagttatacataatgagctggagcaat
+actgccgggcccgcgccggccgctgtcttgaggtgggcgctcacccaagatctattaatg
+ataaccccaatgttctgcaccggtgcttcctccgcccggtcggaagagacgtccagcgtt
+ggtactctgcccccactcgtggcccagcggctaactgccgccgctctgcgctacgcggtt
+tgccccctgtcgatcgcacatactgcttcgacgggttttcccgctgcgcttttgccgcag
+agaccgggattgctctgtactcactgcatgatctttggccctcggacgttgcggaggcta
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
@@ -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
+
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
@@ -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
+
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
@@ -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
+
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
@@ -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
+
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
@@ -0,0 +1,463 @@
+<tool id="varvamp" name="varVAMP" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
+    <description>design primers for highly diverse viruses</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">varvamp</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>
+    </requirements>
+    <version_command>varvamp --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+VARVAMP_CONFIG=custom_config varvamp
+
+$mode.m_select
+#if $mode.main_params.specify_how in ("set_threshold", "set_both"):
+  --threshold $mode.main_params.threshold
+#end if
+#if $mode.main_params.specify_how in ("set_n_ambig", "set_both"):
+  --n-ambig $mode.main_params.n_ambig
+  #if $mode.m_select == "qpcr":
+    --pn-ambig $mode.main_params.pn_ambig
+  #end if
+#end if
+#if str( $mode.m_select ) == "single":
+  --opt-length $mode.opt_length
+  --max-length $mode.max_length
+  #if $mode.limit_report.choice == "yes":
+    --report-n $mode.limit_report.report_n
+  #end if
+#elif str( $mode.m_select ) == "tiled":
+  --opt-length $mode.opt_length
+  --max-length $mode.max_length
+  --overlap $mode.overlap
+#elif str( $mode.m_select ) == "qpcr":
+  --test-n $mode.test_n
+  --deltaG $mode.deltaG
+#end if
+#if $mode.filter_blast_hits.choice == "yes":
+  --database '${mode.filter_blast_hits.database.extra_files_path}/blastdb'
+#end if
+--threads \${GALAXY_SLOTS:-1}
+
+'$alignment'
+results/
+
+#if $mode.m_select == 'qpcr' and $mode.scheme_outputs and 'primer_seqs' in $mode.scheme_outputs:
+  ## make the primer sequences fasta discoverable under the same name that is used in "single" mode
+  && mv results/oligos.fasta results/primers.fasta
+#end if
+#if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs:
+  ## 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
+  && cp -n dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
+#end if
+    ]]></command>
+    <configfiles>
+        <configfile filename="custom_config"><![CDATA[#if $mode.advanced_config.customize == "yes":
+PRIMER_TMP = ($mode.advanced_config.basic_primer_params.PRIMER_TMP_min, $mode.advanced_config.basic_primer_params.PRIMER_TMP_max, $mode.advanced_config.basic_primer_params.PRIMER_TMP_opt)
+PRIMER_GC_RANGE = ($mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_min, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_max, $mode.advanced_config.basic_primer_params.PRIMER_GC_RANGE_opt)
+PRIMER_SIZES = ($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)
+PRIMER_MAX_POLYX = $mode.advanced_config.basic_primer_params.PRIMER_MAX_POLYX
+PRIMER_MAX_DINUC_REPEATS = $mode.advanced_config.basic_primer_params.PRIMER_MAX_DINUC_REPEATS
+PRIMER_HAIRPIN = $mode.advanced_config.basic_primer_params.PRIMER_HAIRPIN
+PRIMER_GC_END = ($mode.advanced_config.basic_primer_params.PRIMER_GC_END_min, $mode.advanced_config.basic_primer_params.PRIMER_GC_END_max)
+PRIMER_MIN_3_WITHOUT_AMB = $mode.advanced_config.basic_primer_params.PRIMER_MIN_3_WITHOUT_AMB
+PRIMER_MAX_DIMER_TMP = $mode.advanced_config.basic_primer_params.PRIMER_MAX_DIMER_TMP
+    #if str($mode.m_select) == "qpcr":
+QPROBE_TMP = ($mode.advanced_config.qpcr_params.QPROBE_TMP_min, $mode.advanced_config.qpcr_params.QPROBE_TMP_max, $mode.advanced_config.qpcr_params.QPROBE_TMP_opt)
+QPROBE_SIZES = ($mode.advanced_config.qpcr_params.QPROBE_SIZES_min, $mode.advanced_config.qpcr_params.QPROBE_SIZES_max, $mode.advanced_config.qpcr_params.QPROBE_SIZES_opt)
+QPROBE_GC_RANGE = ($mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_min, $mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_max, $mode.advanced_config.qpcr_params.QPROBE_GC_RANGE_opt)
+QPROBE_GC_END = ($mode.advanced_config.qpcr_params.QPROBE_GC_END_min, $mode.advanced_config.qpcr_params.QPROBE_GC_END_max)
+QPRIMER_DIFF = $mode.advanced_config.qpcr_params.QPRIMER_DIFF
+QPROBE_TEMP_DIFF = ($mode.advanced_config.qpcr_params.QPROBE_TEMP_DIFF_min, $mode.advanced_config.qpcr_params.QPROBE_TEMP_DIFF_max)
+QPROBE_DISTANCE = ($mode.advanced_config.qpcr_params.QPROBE_DISTANCE_min, $mode.advanced_config.qpcr_params.QPROBE_DISTANCE_max)
+END_OVERLAP = $mode.advanced_config.qpcr_params.END_OVERLAP
+QAMPLICON_LENGTH = ($mode.advanced_config.qpcr_params.QAMPLICON_LENGTH_min, $mode.advanced_config.qpcr_params.QAMPLICON_LENGTH_max)
+QAMPLICON_GC = ($mode.advanced_config.qpcr_params.QAMPLICON_GC_min, $mode.advanced_config.qpcr_params.QAMPLICON_GC_max)
+QAMPLICON_DEL_CUTOFF =  $mode.advanced_config.qpcr_params.QAMPLICON_DEL_CUTOFF
+    #end if
+PCR_MV_CONC = $mode.advanced_config.pcr_params.PCR_MV_CONC
+PCR_DV_CONC = $mode.advanced_config.pcr_params.PCR_DV_CONC
+PCR_DNTP_CONC = $mode.advanced_config.pcr_params.PCR_DNTP_CONC
+PCR_DNA_CONC = $mode.advanced_config.pcr_params.PCR_DNA_CONC
+PRIMER_TM_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_TM_PENALTY
+PRIMER_GC_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_GC_PENALTY
+PRIMER_SIZE_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_SIZE_PENALTY
+PRIMER_MAX_BASE_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_MAX_BASE_PENALTY
+PRIMER_3_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_3_PENALTY
+PRIMER_PERMUTATION_PENALTY = $mode.advanced_config.penalty_multipliers.PRIMER_PERMUTATION_PENALTY
+  #end if
+  #if $mode.filter_blast_hits.choice == "yes":
+    #if $mode.filter_blast_hits.blast_advanced_cond.blast_advanced == "yes":
+BLAST_SETTINGS = {
+    "outfmt": "6 qseqid sseqid qlen length mismatch gapopen sstart send sstrand",
+    "evalue": $mode.filter_blast_hits.blast_advanced_cond.blast_params.evalue,
+    "reward": $mode.filter_blast_hits.blast_advanced_cond.blast_params.reward,
+    "penalty": $mode.filter_blast_hits.blast_advanced_cond.blast_params.penalty,
+    "gapopen": $mode.filter_blast_hits.blast_advanced_cond.blast_params.gapopen,
+    "gapextend": $mode.filter_blast_hits.blast_advanced_cond.blast_params.gapextend
+}
+BLAST_MAX_DIFF = $mode.filter_blast_hits.blast_advanced_cond.blast_hits_usage.BLAST_MAX_DIFF
+BLAST_SIZE_MULTI = $mode.filter_blast_hits.blast_advanced_cond.blast_hits_usage.BLAST_SIZE_MULTI
+BLAST_PENALTY = $mode.filter_blast_hits.blast_advanced_cond.blast_hits_usage.BLAST_PENALTY
+    #end if
+  #end if
+        ]]></configfile>
+        <configfile filename="dimers_fallback.tsv"><![CDATA[#set $line = '\t'.join(['pool', 'primer_name_1', 'primer_name_2', 'dimer melting temp'])
+$line]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="alignment" type="data" format="fasta" label="Multiple alignment of viral sequences" />
+        <conditional name="mode">
+            <param name="m_select" type="select" label="What kind of primers would you like to design? (varvamp mode)">
+                <option value="single">Primers for single amplicons (single)</option>
+                <option value="tiled">Tiled primer scheme for whole-genome sequencing (tiled)</option>
+                <option value="qpcr">qPCR primers (qpcr)</option>
+            </param>
+            <when value="single">
+                <expand macro="main_parameters" />
+                <expand macro="amplicon_length_restrictions" />
+                <expand macro="blast_options" />
+                <conditional name="limit_report">
+                    <param name="choice" type="select" label="Limit the number of amplicons to report?">
+                        <option value="no">No, report all qualifying amplicons</option>
+                        <option value="yes">Yes, set an upper limit on amplicons to be reported</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <param argument="--report-n" type="integer" min="1" value="20" label="Report only the n highest scoring amplicons" />
+                    </when>
+                </conditional>
+                <expand macro="customize_advanced" />
+                <expand macro="primer_scheme_outputs">
+                    <option value="amplicon_assignment">Primer-to-amplicon assignment in tabular format; lists primers belonging to the same amplicon on one line for simpler automated parsing</option>
+                </expand>
+                <expand macro="consensus_outputs" />
+                <expand macro="graphical_outputs" />
+                <expand macro="miscellaneous_outputs">
+                    <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option>
+                </expand>
+            </when>
+            <when value="tiled">
+                <expand macro="main_parameters" />
+                <expand macro="amplicon_length_restrictions" />
+                <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicons" help="default: 100" />
+                <expand macro="blast_options" />
+                <expand macro="customize_advanced" />
+                <expand macro="primer_scheme_outputs">
+                    <option value="amplicon_assignment" selected="true">Primer-to-amplicon assignment in tabular format; lists primers belonging to the same amplicon on one line; required input for automated primer trimming in some downstream analysis workflows</option>
+                    <option value="primer_dimers" selected="true">If any primers in the tiling scheme are predicted to form primer dimers, details about these will be found in this tabular output.</option>
+                </expand>
+                <expand macro="consensus_outputs" />
+                <expand macro="graphical_outputs" />
+                <expand macro="miscellaneous_outputs">
+                    <option value="all_primers">Binding sites of ALL high-scoring primers that were considered in BED format; includes primer penalties (lower is better) as the score column</option>
+                </expand>
+            </when>
+            <when value="qpcr">
+                <expand macro="main_parameters">
+                    <param argument="--pn-ambig" type="integer" min="0" value="1" label="Maximum number of ambiguous nucleotides per qPCR probe to be tolerated" help="To enforce specificity of detection, varVAMP will refuse to work if you set this value higher than for the amplicon primers above, and you may actually want to set it slightly lower than that value." />
+                </expand>
+                <param argument="--test-n" type="integer" min="1" value="50" label="Top n qPCR amplicons to test" help="test the top n qPCR amplicons for secondary structures at the minimal primer temperature. (default: 50)" />
+                <param argument="--deltaG" type="integer" value="-3" label="Minimum free energy (kcal/mol/K) cutoff" help="Minimum free energy (kcal/mol/K) cutoff at the lowest primer melting temperature. (default: -3." />
+                <expand macro="blast_options" />
+                <expand macro="customize_advanced">
+                    <section name="qpcr_params" title="Constraints on qPCR probes and amplicons" expanded="false">
+                        <!--basic probe parameters-->
+                        <param name="QPROBE_TMP_min" type="integer" min="0" value="64" label="Minimal qPCR probe melting temperature" help="With varVAMP default settings, the probe melting temperatures are 7°C higher than those of amplicon primers." />
+                        <param name="QPROBE_TMP_max" type="integer" min="0" value="70" label="Maximal qPCR probe melting temperature" help="With varVAMP default settings, the probe melting temperatures are 7°C higher than those of amplicon primers." />
+                        <param name="QPROBE_TMP_opt" type="integer" min="0" value="67" label="Optimal qPCR probe melting temperature" help="With varVAMP default settings, the probe melting temperatures are 7°C higher than those of amplicon primers." />
+                        <param name="QPROBE_SIZES_min" type="integer" min="0" value="20" label="Minimal qPCR probe size" />
+                        <param name="QPROBE_SIZES_max" type="integer" min="0" value="30" label="Maximal qPCR probe size" />
+                        <param name="QPROBE_SIZES_opt" type="integer" min="0" value="25" label="Optimal qPCR probe size" />
+                        <param name="QPROBE_GC_RANGE_min" type="integer" min="0" max="100" value="40" label="Minimal qPCR probe GC-content" />
+                        <param name="QPROBE_GC_RANGE_max" type="integer" min="0" max="100" value="80" label="Maximal qPCR probe GC-content" />
+                        <param name="QPROBE_GC_RANGE_opt" type="integer" min="0" max="100" value="60" label="Optimal qPCR probe GC-content" />
+                        <param name="QPROBE_GC_END_min" type="integer" min="0" max="5" value="0" label="Minimal number of GCs among the 3'-terminal 5 bases of the probe" />
+                        <param name="QPROBE_GC_END_max" type="integer" min="0" max="5" value="4" label="Maximal number of GCs among the 3'-terminal 5 bases of the probe" />
+                        <!--constraints for amplicon design-->
+                        <param name="QPRIMER_DIFF" type="integer" min="0" max="10" value="2" label="Maximal melting temperature difference among qPCR primers" />
+                        <param name="QPROBE_TEMP_DIFF_min" type="integer" min="0" max="20" value="5" label="Minimal melting temperature difference between qPCR probe and primers" />
+                        <param name="QPROBE_TEMP_DIFF_max" type="integer" min="0" max="20" value="10" label="Maximal melting temperature difference between qPCR probe and primers" />
+                        <param name="QPROBE_DISTANCE_min" type="integer" min="0" max="20" value="4" label="Minimal distance of the qPCR probe from the primer on the same strand" />
+                        <param name="QPROBE_DISTANCE_max" type="integer" min="0" max="20" value="15" label="Maximal distance of the qPCR probe from the primer on the same strand" />
+                        <param name="END_OVERLAP" type="integer" min="0" max="10" value="5" label="End Overlap" help="Maximal overlap in bases between the ends of the qPCR probe and the primer on the opposite strand" />
+                        <param name="QAMPLICON_LENGTH_min" type="integer" min="0" max="300" value="70" label="Minimal length of qPCR amplicons" />
+                        <param name="QAMPLICON_LENGTH_max" type="integer" min="0" max="300" value="200" label="Maximal length of qPCR amplicons" />
+                        <param name="QAMPLICON_GC_min" type="integer" min="0" max="100" value="40" label="Minimal GC-content of qPCR amplicons" />
+                        <param name="QAMPLICON_GC_max" type="integer" min="0" max="100" value="60" label="Maximal GC-content of qPCR amplicons" />
+                        <param name="QAMPLICON_DEL_CUTOFF" type="integer" min="0" max="10" value="4" label="Cutoff for deletions allowed in aligned regions under qPCR amplicons" help ="qPCR amplicon candidates are not considered further if they span regions of the alignment that contain deletions as long as this cutoff in bases, or longer."/>
+                    </section>
+                </expand>
+                <expand macro="primer_scheme_outputs">
+                    <option value="qpcr_design" selected="true">qPCR amplicon details in tabular format</option>
+                </expand>
+                <expand macro="consensus_outputs" />
+                <expand macro="graphical_outputs" />
+                <expand macro="miscellaneous_outputs">
+                    <option value="probe_regions">List of all candidate regions of the consensus sequence that were evaluated for qPCR probes in BED format</option>
+                </expand>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="varvamp_log" format="txt" from_work_dir="results/varvamp_log.txt" label="${tool.name} on ${on_string}: Analysis Log" />
+        <data name="primer_seqs" format="fasta" from_work_dir="results/primers.fasta" label="${tool.name} on ${on_string}: Sequences of designed oligos">
+            <filter>mode['m_select'] in ('single', 'qpcr') and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
+        </data>
+        <collection name="primer_seqs_collection" type="list" label="${tool.name} on ${on_string}: per-pool primer sequences">
+            <filter>mode['m_select'] == 'tiled' and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
+            <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_0.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" />
+            <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" />
+        </collection>
+        <data name="primers_bed" format="bed" from_work_dir="results/primers.bed" label="${tool.name} on ${on_string}: Primer binding sites">
+            <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter>
+        </data>
+        <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations">
+            <filter>mode['scheme_outputs'] and 'amplicon_sites' in mode['scheme_outputs']</filter>
+        </data>
+        <data name="primers_details" format="tabular" from_work_dir="results/*primers.tsv" label="${tool.name} on ${on_string}: Primer details">
+            <filter>mode['scheme_outputs'] and 'primer_details' in mode['scheme_outputs']</filter>
+        </data>
+        <data name="qpcr_details" format="tabular" from_work_dir="results/qpcr_design.tsv" label="${tool.name} on ${on_string}: qPCR amplicon details" >
+            <filter>mode['scheme_outputs'] and 'qpcr_design' in mode['scheme_outputs']</filter>
+        </data>
+        <data name="primer_amplicon_assignments" format="tabular" from_work_dir="results/primer_to_amplicon_assignment.tabular" label="${tool.name} on ${on_string}: Primer to amplicon assignments">
+            <filter>mode['scheme_outputs'] and 'amplicon_assignment' in mode['scheme_outputs']</filter>
+        </data>
+        <data name="unresolved_primer_dimers" format="tabular" from_work_dir="results/unsolvable_primer_dimers.tsv" label="${tool.name} on ${on_string}: Unresolved primer dimers">
+            <filter>mode['scheme_outputs'] and 'primer_dimers' in mode['scheme_outputs']</filter>
+        </data>
+        <data name="ambiguous_consensus" format="fasta" from_work_dir="results/ambiguous_consensus.fasta" label="${tool.name} on ${on_string}: Ambiguous consensus sequence">
+            <filter>mode['aln_cons_outputs'] and 'ambiguous_consensus' in mode['aln_cons_outputs']</filter>
+        </data>
+        <data name="majority_consensus" format="fasta" from_work_dir="results/data/majority_consensus.fasta" label="${tool.name} on ${on_string}: Majority consensus sequence (no ambiguity codes)">
+            <filter>mode['aln_cons_outputs'] and 'majority_consensus' in mode['aln_cons_outputs']</filter>
+        </data>
+        <data name="alignment_cleaned" format="fasta" from_work_dir="results/data/alignment_cleaned.fasta" label="${tool.name} on ${on_string}: Alignment cleaned">
+            <filter>mode['aln_cons_outputs'] and 'alignment_cleaned' in mode['aln_cons_outputs']</filter>
+        </data>
+        <data name="amplicon_plot" format="pdf" from_work_dir="results/amplicon_plot.pdf" label="${tool.name} on ${on_string}: Amplicon design overview plot">
+            <filter>mode['plot_outputs'] and 'amplicon_plot' in mode['plot_outputs']</filter>
+        </data>
+        <data name="per_base_mismatches" format="pdf" from_work_dir="results/per_base_mismatches.pdf" label="${tool.name} on ${on_string}: Per-base mismatches barplots">
+            <filter>mode['plot_outputs'] and 'per_base_mismatches' in mode['plot_outputs']</filter>
+        </data>
+        <data name="primer_regions" format="bed" from_work_dir="results/data/primer_regions.bed" label="${tool.name} on ${on_string}: All candidate primer regions">
+            <filter>mode['misc_outputs'] and 'primer_regions' in mode['misc_outputs']</filter>
+        </data>
+        <data name="probe_regions" format="bed" from_work_dir="results/data/probe_regions.bed" label="${tool.name} on ${on_string}: All candidate qPCR probe regions">
+            <filter>mode['misc_outputs'] and 'probe_regions' in mode['misc_outputs']</filter>
+        </data>
+        <data name="all_primers" format="bed" from_work_dir="results/data/all_primers.bed" label="${tool.name} on ${on_string}: All primer sites">
+            <filter>mode['misc_outputs'] and 'all_primers' in mode['misc_outputs']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="8">
+            <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>
+            <conditional name="mode">
+                <param name='m_select' value="single"/>
+                <conditional name="main_params">
+                    <param name="specify_how" value="set_both"/>
+                    <param name="threshold" value="0.8"/>
+                    <param name="n_ambig" value="3"/>
+                </conditional>
+                <param name="opt_length" value="300"/>
+                <param name="max_length" value="400"/>
+                <conditional name="limit_report">
+                    <param name="choice" value="yes" />
+                    <param name="report_n" value="5"/>
+                </conditional>
+            </conditional>
+            <output name="varvamp_log" ftype="txt" compare="contains" file="test1.log" />
+            <output name="ambiguous_consensus" ftype="fasta" file="ambiguous_consensus.fasta" />
+            <output name="amplicon_plot" ftype="pdf">
+                <assert_contents>
+                    <has_text text="%PDF"/>
+                    <has_text text="%%EOF"/>
+                </assert_contents>
+            </output>
+            <output name="primers_bed" ftype="bed">
+                <assert_contents>
+                    <has_n_lines n="2" />
+                </assert_contents>
+            </output>
+            <output name="amplicons_bed" ftype="bed">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+            <output name="per_base_mismatches" ftype="pdf">
+                <assert_contents>
+                    <has_text text="%PDF"/>
+                    <has_text text="%%EOF"/>
+                </assert_contents>
+            </output>
+            <output name="primer_seqs" ftype="fasta">
+                <assert_contents>
+                    <has_line line=">AMPLICON_0_LEFT"/>
+                    <has_line line=">AMPLICON_0_RIGHT"/>
+                    <has_n_lines n="4"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="12">
+            <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>
+            <conditional name="mode">
+                <param name='m_select' value="tiled"/>
+                <conditional name="main_params">
+                    <param name="specify_how" value="set_both"/>
+                    <param name="threshold" value="0.6"/>
+                    <param name="n_ambig" value="2"/>
+                </conditional>
+                <param name="opt_length" value="150"/>
+                <param name="max_length" value="300"/>
+                <param name="overlap" value="100"/>
+            </conditional>
+            <output name="varvamp_log" ftype="txt" compare="contains" file="test2.log" />
+            <output name="primers_bed" ftype="bed">
+                <assert_contents>
+                    <has_n_lines n="4" />
+                </assert_contents>
+            </output>
+            <output name="amplicons_bed" ftype="bed">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+            <output name="primer_amplicon_assignments" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+            <output name="unresolved_primer_dimers" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+            <output_collection name="primer_seqs_collection" type="list" count="2">
+                <element name="pool1_sequences" ftype="fasta">
+                    <assert_contents>
+                        <has_n_lines n="4"/>
+                        <has_line line=">AMPLICON_0_LEFT"/>
+                    </assert_contents>
+                </element>
+                <element name="pool2_sequences" ftype="fasta">
+                    <assert_contents>
+                        <has_n_lines n="4"/>
+                        <has_line line=">AMPLICON_1_LEFT"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test expect_num_outputs="9">
+            <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>
+            <conditional name="mode">
+                <param name='m_select' value="qpcr"/>
+                <conditional name="main_params">
+                    <param name="specify_how" value="set_both"/>
+                    <param name="threshold" value="0.7"/>
+                    <param name="n_ambig" value="1"/>
+                    <param name="pn_ambig" value="1"/>
+                </conditional>
+                <param name="test_n" value="180"/>
+                <param name="deltaG" value="-15"/>
+            </conditional>
+            <output name="varvamp_log" ftype="txt" compare="contains" file="test3.log" />
+            <output name="primers_bed" ftype="bed">
+                <assert_contents>
+                    <has_n_lines n="3" />
+                </assert_contents>
+            </output>
+            <output name="amplicons_bed" ftype="bed">
+                <assert_contents>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+            <output name="primer_seqs" ftype="fasta">
+                <assert_contents>
+                    <has_line line=">QPCR_SCHEME_0_PROBE"/>
+                    <has_line line=">QPCR_SCHEME_0_LEFT"/>
+                    <has_line line=">QPCR_SCHEME_0_RIGHT"/>
+                    <has_n_lines n="6"/>
+                </assert_contents>
+            </output>
+            <output name="qpcr_details" ftype="tabular">
+                <assert_contents>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <!-- Similar to test 1, but try to modify some of varVAMP's
+            advanced params, and see whether that gets reflected in the log file.
+            -->
+            <param name="alignment" value="hepatitis_e_aln_shrunk.fasta"/>
+            <conditional name="mode">
+                <param name='m_select' value="single"/>
+                <conditional name="main_params">
+                    <param name="specify_how" value="set_both"/>
+                    <param name="threshold" value="0.8"/>
+                    <param name="n_ambig" value="3"/>
+                </conditional>
+                <param name="opt_length" value="300"/>
+                <param name="max_length" value="400"/>
+                <conditional name="limit_report">
+                    <param name="choice" value="yes" />
+                    <param name="report_n" value="5"/>
+                </conditional>
+                <conditional name="advanced_config">
+                    <param name="customize" value="yes"/>
+                    <section name="basic_primer_params">
+                        <param name="PRIMER_GC_RANGE_min" value="20"/>
+                        <param name="PRIMER_GC_RANGE_max" value="80"/>
+                    </section>
+                </conditional>
+                <param name="scheme_outputs" value=""/>
+                <param name="aln_cons_outputs" value=""/>
+                <param name="plot_outputs" value=""/>
+                <param name="misc_outputs" value=""/>
+            </conditional>
+            <output name="varvamp_log" ftype="txt" compare="contains" file="test4.log" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences.
+
+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.
+
+varVAMP can be run in three different **modes**:
+
+* SINGLE: varVAMP searches for the very best primers and reports back non-overlapping amplicons which can be used for PCR-based screening approaches.
+* 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.
+* 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.
+
+Algorithmic parameters:
+
+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.
+
+Outputs:
+
+This tool can produce lots of informative output and the different modes come with what we hope are reasonable default choices.
+
+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.
+
+.. class:: infomark
+
+Testing with a new alignment/analysis:
+
+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.
+    ]]></help>
+    <citations>
+        <citation type="doi">https://github.com/jonas-fuchs/varVAMP/</citation>
+    </citations>
+</tool>