# HG changeset patch
# User iuc
# Date 1741548433 0
# Node ID 871214ac722eda01b72d781512c32efe272299de
# Parent  356bec18c68da9a0e7b6f3b3670ce03ce4343e02
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam commit 8eca6c026e7bd7ab2e471485cb93b8dee1cd2c07

diff -r 356bec18c68d -r 871214ac722e decontam.xml
--- a/decontam.xml	Mon Dec 09 16:04:03 2024 +0000
+++ b/decontam.xml	Sun Mar 09 19:27:13 2025 +0000
@@ -1,4 +1,5 @@
 <tool id="decontam" name="Decontam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Identification and removal of contaminants</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -150,6 +151,18 @@
    Currently, only the negative control sample method is implemented in this
    wrapper.
 
+**Method**
+
+To identify contaminants decontam requires a defined set of “negative control” samples in
+ which sequencing was performed on blanks without any biological sample added. 
+Extraction controls are preferred, and in amplicon sequencing the negative controls
+ should also be carried through the PCR step, as each step in the workflow 
+ has the potential to introduce new contaminants.
+
+Decontam then uses Fisher’s exact tests to detect weather a feature is a contaminant or not,
+by comparing true samples to ngeative controls. For more details on the detection method see 
+the publication of decontam.
+
 **Output**
 
 - If a phyloseq object is provided as input, the output will be a phyloseq