# HG changeset patch
# User iuc
# Date 1718466208 0
# Node ID 36c91ff33d70f38536f390f949337f16bb6cea24
# Parent  33fac436dd545f63548e5a12d71a8188f3dfe63a
planemo upload for repository https://github.com/jonas-fuchs/varVAMP commit 11f2603dc33eecd4fb6f6239143d13c53492fd86

diff -r 33fac436dd54 -r 36c91ff33d70 macros.xml
--- a/macros.xml	Wed May 08 07:05:53 2024 +0000
+++ b/macros.xml	Sat Jun 15 15:43:28 2024 +0000
@@ -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?">
@@ -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." />
diff -r 33fac436dd54 -r 36c91ff33d70 varvamp.xml
--- a/varvamp.xml	Wed May 08 07:05:53 2024 +0000
+++ b/varvamp.xml	Sat Jun 15 15:43:28 2024 +0000
@@ -179,17 +179,17 @@
                         <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">