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comparison ivar_consensus.xml @ 13:1069f6db0a0e draft

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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
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12:9c5754002592 13:1069f6db0a0e
1 <tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 1 <tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>Call consensus from aligned BAM file</description> 2 <description>Call consensus from aligned BAM file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
11 ln -s '$input_bam' sorted.bam && 11 ln -s '$input_bam' sorted.bam &&
12 samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus 12 samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus
13 -p consensus 13 -p consensus
14 -q $min_qual 14 -q $min_qual
15 -t $min_freq 15 -t $min_freq
16 -c $min_indel_freq
16 -m $min_depth 17 -m $min_depth
17 $depth_action 18 $depth_action
18 && 19 &&
19 sed -i "s|consensus|$clean_name|" consensus.fa 20 sed -i "s|consensus|$clean_name|" consensus.fa
20 ]]></command> 21 ]]></command>
32 0.9 - Strict or bases that make up atleast 90% of the depth at a position <br/> 33 0.9 - Strict or bases that make up atleast 90% of the depth at a position <br/>
33 1 - Identical or bases that make up 100% of the depth at a position. Will have highest ambiguities 34 1 - Identical or bases that make up 100% of the depth at a position. Will have highest ambiguities
34 ]]> 35 ]]>
35 </help> 36 </help>
36 </param> 37 </param>
38 <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."/>
37 <param name="min_depth" argument="-m" type="integer" min="1" max="255" value="10" label="Minimum depth to call consensus"/> 39 <param name="min_depth" argument="-m" type="integer" min="1" max="255" value="10" label="Minimum depth to call consensus"/>
38 <param name="depth_action" type="select" label="How to represent positions with coverage less than the minimum depth threshold"> 40 <param name="depth_action" type="select" label="How to represent positions with coverage less than the minimum depth threshold">
39 <option value="-k">Drop from output (-k)</option> 41 <option value="-k">Drop from output (-k)</option>
40 <option value="-n N" selected="true">Represent as N (-n N)</option> 42 <option value="-n N" selected="true">Represent as N (-n N)</option>
41 <option value="-n -">Represent as - (-n -)</option> 43 <option value="-n -">Represent as - (-n -)</option>
58 60
59 The command formed by this wrapper is : 61 The command formed by this wrapper is :
60 62
61 samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus [options] 63 samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus [options]
62 64
63 There are four parameters that can be set: 65 There are five parameters that can be set:
64 66
65 - **Minimum quality**: the minimum quality of a base to be considered in calculations of variant frequencies at a given position 67 - **Minimum quality**: the minimum quality of a base to be considered in calculations of variant frequencies at a given position
66 68
67 - **Minimum frequency threshold**: the minimum frequency that the most likely base must surpass to be called as the consensus base at a position. 69 - **Minimum frequency threshold**: the minimum frequency that the most likely base must surpass to be called as the consensus base at a position.
68 70
71 - **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.
72
69 - **Minimum depth to call consensus**: the minimum required depth to call a consensus base 73 - **Minimum depth to call consensus**: the minimum required depth to call a consensus base
70 74
71 - **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: 75 - **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:
72 76
73 - Drop the position from the output entirely (-> the consensus sequence can become shorter than the reference used to produce the input BAM!) 77 - Drop the position from the output entirely (-> the consensus sequence can become shorter than the reference used to produce the input BAM!)