Mercurial > repos > iuc > dada2_removebimeradenovo

changeset 11:efe26de231ec draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit bbbc0e71b1db299a7c7296f25ac7adcccd27fbe3
author iuc
date Tue, 11 Feb 2025 23:28:29 +0000
parents 1770d188f72d
children
files dada2_removeBimeraDenovo.xml macros.xml
diffstat 2 files changed, 7 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/dada2_removeBimeraDenovo.xml	Sat Dec 07 08:47:32 2024 +0000
+++ b/dada2_removeBimeraDenovo.xml	Tue Feb 11 23:28:29 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="dada2_removeBimeraDenovo" name="dada2: removeBimeraDenovo" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
+<tool id="dada2_removeBimeraDenovo" name="dada2: removeBimeraDenovo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Remove bimeras from collections of unique sequences</description>
     <macros>
         <import>macros.xml</import>
@@ -82,6 +82,8 @@
 - from **pooled** sequences: Each sequence is evaluated against a set of "parents" drawn from the sequence collection that are sufficiently more abundant than the sequence being evaluated. Sequences that are bimera are removed, i.e. a two-parent chimera, in which the left side is made up of one parent sequence, and the right-side made up of a second parent sequence.
 - by **consensus**: In short, bimeric sequences are flagged on a sample-by-sample basis. Then, a vote is performed for each sequence across all samples in which it appeared. If the sequence is flagged in a sufficiently high fraction of samples, it is identified as a bimera. A logical vector is returned, with an entry for each sequence in the table indicating whether it was identified as bimeric by this consensus procedure.
 
+**Note**: pooled should only be used in combination with pooled denoising.
+
 Usage
 .....
 
--- a/macros.xml	Sat Dec 07 08:47:32 2024 +0000
+++ b/macros.xml	Tue Feb 11 23:28:29 2025 +0000
@@ -2,7 +2,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">bioconductor-dada2</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -12,8 +12,9 @@
             <xref type="bioconductor">dada2</xref>
         </xrefs>
     </xml>
-    <token name="@DADA2_VERSION@">1.30.0</token>
-    <token name="@WRAPPER_VERSION@">0</token>
+    <token name="@PROFILE@">23.2</token>
+    <token name="@TOOL_VERSION@">1.34.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="version_command">
         <version_command><![CDATA[