Update varVAMP to v1.2.0 (galaxyproject#5995)

bebatut · May 8, 2024 · 1056d5c · 1056d5c
1 parent 5fd8f13
commit 1056d5c
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Showing 2 changed files with 1 addition and 3 deletions.
diff --git a/tools/varvamp/macros.xml b/tools/varvamp/macros.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.1.3</token>
+    <token name="@TOOL_VERSION@">1.2.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="main_parameters">
         <conditional name="main_params">
@@ -53,7 +53,6 @@
                         <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>

diff --git a/tools/varvamp/varvamp.xml b/tools/varvamp/varvamp.xml
@@ -103,7 +103,6 @@ BLAST_SETTINGS = {
 }
 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>