Mercurial > repos > iuc > ivar_consensus

annotate ivar_consensus.xml @ 12:9c5754002592 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit fc9887dd2a1468b58a5da12a91fe3fbcd226e981
author iuc
date Fri, 10 Feb 2023 17:06:13 +0000
parents 3e4f434a69c6
children 1069f6db0a0e
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12
9c5754002592 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit fc9887dd2a1468b58a5da12a91fe3fbcd226e981
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1 <tool id="ivar_consensus" name="ivar consensus" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
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2 <description>Call consensus from aligned BAM file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10 #set $clean_name = re.sub('[^\w\-]', '_', str($input_bam.element_identifier))
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11 ln -s '$input_bam' sorted.bam &&
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9c5754002592 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit fc9887dd2a1468b58a5da12a91fe3fbcd226e981
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12 samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus
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13 -p consensus
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14 -q $min_qual
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15 -t $min_freq
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16 -m $min_depth
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17 $depth_action
0
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18 &&
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19 sed -i "s|consensus|$clean_name|" consensus.fa
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20 ]]></command>
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21 <inputs>
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22 <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
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23 <!-- Warning: integer params in the following define a max of 255 intentionally
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24 because the underlying C++ code of ivar defines them as uint8 and does not check for overflow! -->
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25 <param name="min_qual" argument="-q" type="integer" min="0" max="255" value="20" label="Minimum quality score threshold to count base"/>
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26 <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.0" label="Minimum frequency threshold">
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27 <help>
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28 <![CDATA[
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29 0 - Majority or most common base <br/>
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30 0.2 - Bases that make up atleast 20% of the depth at a position <br/>
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31 0.5 - Strict or bases that make up atleast 50% of the depth at a position <br/>
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32 0.9 - Strict or bases that make up atleast 90% of the depth at a position <br/>
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33 1 - Identical or bases that make up 100% of the depth at a position. Will have highest ambiguities
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34 ]]>
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35 </help>
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36 </param>
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37 <param name="min_depth" argument="-m" type="integer" min="1" max="255" value="10" label="Minimum depth to call consensus"/>
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38 <param name="depth_action" type="select" label="How to represent positions with coverage less than the minimum depth threshold">
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39 <option value="-k">Drop from output (-k)</option>
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40 <option value="-n N" selected="true">Represent as N (-n N)</option>
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41 <option value="-n -">Represent as - (-n -)</option>
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42 </param>
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43 </inputs>
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44 <outputs>
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45 <data name="consensus" format="fasta" label="${tool.name} on ${on_string} Consensus" from_work_dir="consensus.fa"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="input_bam" value="covid19/PC00101P_sub.trimmed.sorted.bam" />
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50 <output name="consensus" file="covid19/PC00101P_sub.fa" ftype="fasta" compare="contains" lines_diff="1"/>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54 .. class:: infomark
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55
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56 To generate a consensus sequence iVar uses the output of samtools mpileup
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57 command. The mpileup output must be piped into ivar consensus
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58
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59 The command formed by this wrapper is :
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60
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61 samtools mpileup -A -a -d 0 -Q 0 sorted.bam | ivar consensus [options]
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62
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63 There are four parameters that can be set:
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64
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65 - **Minimum quality**: the minimum quality of a base to be considered in calculations of variant frequencies at a given position
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66
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67 - **Minimum frequency threshold**: the minimum frequency that the most likely base must surpass to be called as the consensus base at a position.
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68
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69 - **Minimum depth to call consensus**: the minimum required depth to call a consensus base
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70
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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:
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72
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73 - Drop the position from the output entirely (-> the consensus sequence can become shorter than the reference used to produce the input BAM!)
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74 - Use an ``N``, or
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75 - Use a ``-`` to represent the position
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76 ]]> </help>
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77 <expand macro="citations" />
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78 </tool>