Skip to content

Commit

Permalink
Remove arbitrary upper limits on some qPCR parameters (#6084)
Browse files Browse the repository at this point in the history 
* Remove arbitrary upper limits on some qPCR parameters

* No upper limit for PRIMER_TM_PENALTY
  • Loading branch information
@wm75
wm75 authored Jun 15, 2024
1 parent 24d62a0 commit 11f2603
Show file tree
Hide file tree
Showing 2 changed files with 11 additions and 11 deletions.
4 changes: 2 additions & 2 deletions tools/varvamp/macros.xml
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">1.2.0</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<xml name="main_parameters">
<conditional name="main_params">
<param name="specify_how" type="select" label="How to set the main parameters, threshold for consensus nucleotides and max ambiguous nts per primer?">
Expand Down Expand Up @@ -93,7 +93,7 @@
<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_TM_PENALTY" type="float" min="0" value="2" label="Temperature penalty multiplier" help="Each °C deviation of primer melting temperature from the configured optimal melting temperature inflicts a penalty of this size." />
<param name="PRIMER_GC_PENALTY" type="float" min="0" value="0.2" label="GC-content penalty multiplier" help="Each % deviation of primer GC-content from the configured optimal GC-content inflicts a penalty of this size." />
<param name="PRIMER_SIZE_PENALTY" type="float" min="0" value="0.5" label="Primer size penalty multiplier" help="Each base deviation of primer length from the configured optimal length inflicts a penalty of this size."/>
<param name="PRIMER_MAX_BASE_PENALTY" type="integer" min="0" value="10" label="Maximal primer base penalty" help="Primer base penalty is the sum of the primer's temperature, GC-content and size penalties as defined above. If that base penalty exceeds the maximum defined here, the candidate primer gets discarded and is not considered further." />
Expand Down
18 changes: 9 additions & 9 deletions tools/varvamp/varvamp.xml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -179,17 +179,17 @@ $line]]></configfile>
<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="QPRIMER_DIFF" type="integer" min="0" value="2" label="Maximal melting temperature difference among qPCR primers" />
<param name="QPROBE_TEMP_DIFF_min" type="integer" min="0" value="5" label="Minimal melting temperature difference between qPCR probe and primers" />
<param name="QPROBE_TEMP_DIFF_max" type="integer" min="0" value="10" label="Maximal melting temperature difference between qPCR probe and primers" />
<param name="QPROBE_DISTANCE_min" type="integer" min="0" 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" value="15" label="Maximal distance of the qPCR probe from the primer on the same strand" />
<param name="END_OVERLAP" type="integer" min="0" 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" value="70" label="Minimal length of qPCR amplicons" />
<param name="QAMPLICON_LENGTH_max" type="integer" min="0" 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."/>
<param name="QAMPLICON_DEL_CUTOFF" type="integer" min="0" 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">
Expand Down

0 comments on commit 11f2603

Please sign in to comment.