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comparison decontam.xml @ 3:871214ac722e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/decontam commit 8eca6c026e7bd7ab2e471485cb93b8dee1cd2c07
author iuc
date Sun, 09 Mar 2025 19:27:13 +0000
parents 86da5c894956
children
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2:356bec18c68d 3:871214ac722e
1 <tool id="decontam" name="Decontam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="decontam" name="Decontam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Identification and removal of contaminants</description>
2 <macros> 3 <macros>
3 <import>macros.xml</import> 4 <import>macros.xml</import>
4 </macros> 5 </macros>
5 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
148 .. note:: 149 .. note::
149 150
150 Currently, only the negative control sample method is implemented in this 151 Currently, only the negative control sample method is implemented in this
151 wrapper. 152 wrapper.
152 153
154 **Method**
155
156 To identify contaminants decontam requires a defined set of “negative control” samples in
157 which sequencing was performed on blanks without any biological sample added.
158 Extraction controls are preferred, and in amplicon sequencing the negative controls
159 should also be carried through the PCR step, as each step in the workflow
160 has the potential to introduce new contaminants.
161
162 Decontam then uses Fisher’s exact tests to detect weather a feature is a contaminant or not,
163 by comparing true samples to ngeative controls. For more details on the detection method see
164 the publication of decontam.
165
153 **Output** 166 **Output**
154 167
155 - If a phyloseq object is provided as input, the output will be a phyloseq 168 - If a phyloseq object is provided as input, the output will be a phyloseq
156 object pruned to include only non-contaminant features. 169 object pruned to include only non-contaminant features.
157 - If only the feature table or metadata is provided, the output will be a 170 - If only the feature table or metadata is provided, the output will be a