Mercurial > repos > iuc > ivar_consensus
diff ivar_consensus.xml @ 13:1069f6db0a0e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
| author | iuc |
|---|---|
| date | Mon, 13 Feb 2023 17:30:23 +0000 |
| parents | 9c5754002592 |
| children | e4ee04da1c19 |
line wrap: on
line diff
--- a/ivar_consensus.xml Fri Feb 10 17:06:13 2023 +0000 +++ b/ivar_consensus.xml Mon Feb 13 17:30:23 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> +<tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> <description>Call consensus from aligned BAM file</description> <macros> <import>macros.xml</import> @@ -13,6 +13,7 @@ -p consensus -q $min_qual -t $min_freq + -c $min_indel_freq -m $min_depth $depth_action && @@ -34,6 +35,7 @@ ]]> </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 "Minimum frequency threshold" 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="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> @@ -60,12 +62,14 @@ samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus [options] - There are four parameters that can be set: + There are five parameters that can be set: - **Minimum quality**: the minimum quality of a base to be considered in calculations of variant frequencies at a given position - **Minimum frequency threshold**: the minimum frequency that the most likely base must surpass to be called as the consensus base at a position. - + + - **Minimum indel frequency threshold**: has the same meaning as the previous threshold, but gets applied to indels specifically. Setting this threshold higher than the threshold applied to SNVs helps reduce indel artefacts in the generated consensus. + - **Minimum depth to call consensus**: the minimum required depth to call a consensus base - **How to represent positions with coverage less than the minimum depth threshold**: for positions for which the above minimum depth to call a consensus base is not reached, you can choose one of three different actions: