Mercurial > repos > iuc > ivar_consensus

changeset 14:e4ee04da1c19 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 3839802e0a790cb519cffdc2d8a6b92d73e4c9ef
author iuc
date Sat, 25 Mar 2023 12:53:47 +0000
parents 1069f6db0a0e
children ede363a64152
files ivar_consensus.xml macros.xml
diffstat 2 files changed, 3 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/ivar_consensus.xml	Mon Feb 13 17:30:23 2023 +0000
+++ b/ivar_consensus.xml	Sat Mar 25 12:53:47 2023 +0000
@@ -21,8 +21,6 @@
     ]]></command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
-        <!-- Warning: integer params in the following define a max of 255 intentionally
-        because the underlying C++ code of ivar defines them as uint8 and does not check for overflow! -->
         <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality score threshold to count base"/>
         <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.0" label="Minimum frequency threshold">
             <help>
@@ -36,7 +34,7 @@
             </help>
         </param>
         <param name="min_indel_freq" argument="-c" type="float" min="0" max="1" value="0.8" label="Minimum indel frequency threshold" help="Same meaning as the &quot;Minimum frequency threshold&quot; above, but applied to indels."/>
-        <param name="min_depth" argument="-m" type="integer" min="1" max="255" value="10" label="Minimum depth to call consensus"/>
+        <param name="min_depth" argument="-m" type="integer" min="1" value="10" label="Minimum depth to call consensus"/>
         <param name="depth_action" type="select" label="How to represent positions with coverage less than the minimum depth threshold">
             <option value="-k">Drop from output (-k)</option>
             <option value="-n N" selected="true">Represent as N (-n N)</option>
--- a/macros.xml	Mon Feb 13 17:30:23 2023 +0000
+++ b/macros.xml	Sat Mar 25 12:53:47 2023 +0000
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
 <macros>
-  <token name="@TOOL_VERSION@">1.3.2</token>
+  <token name="@TOOL_VERSION@">1.4.0</token>
   <token name="@PROFILE@">21.01</token>
   <xml name="requirements">
   <requirements>
       <requirement type="package" version="@TOOL_VERSION@">ivar</requirement>
-      <requirement type="package" version="3.10.8">python</requirement>
+      <requirement type="package" version="3.11.0">python</requirement>
       <requirement type="package" version="1.16.1">samtools</requirement>
       <yield/>
   </requirements>