Mercurial > repos > nick > sequence_content_trimmer

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"planemo upload commit 8e52aac4afce4ab7c4d244e2b70f205f70c16749-dirty"
author nick
date Fri, 27 May 2022 23:29:45 +0000
parents 7f170cb06e2e
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1 <?xml version="1.0"?>
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2 <tool id="sequence_content_trimmer" version="0.2.3" name="Sequence Content Trimmer">
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3 <description>trim reads based on certain bases</description>
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4 <command detect_errors="exit_code"><![CDATA[
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5 #if $paired.is_paired and (('fasta' in $input1.extension and 'fastq' in $input2.extension) or \
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6 ('fastq' in $input1.extension and 'fasta' in $input2.extension))
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7 echo 'Both input files must be either fastq or fasta (no mixing the two).' >&2
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8 #else
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9 python '$__tool_directory__/trimmer.py' '$input1'
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10 #if $paired.is_paired:
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11 '$input2' '$output1' '$output2'
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12 #end if
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13 #if $input1.extension in ('fastq', 'fastqsanger', 'fastqillumina', 'fastqsolexa')
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14 -f fastq
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15 #elif $input1.extension == 'fasta'
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16 -f fasta
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17 #else
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18 -f '$input1.extension'
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19 #end if
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20 -b '$bases' -t '$thres' -w '$win_len' $invert
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21 #if $min_len.has_min_len:
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22 -m '$min_len.value'
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23 #end if
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24 #if not $paired.is_paired:
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25 > '$output1'
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26 #end if
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27 #end if
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28 ]]>
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29 </command>
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30 <inputs>
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31 <conditional name="paired">
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32 <param name="is_paired" type="select" label="Paired reads?">
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33 <option value="" selected="True">Unpaired</option>
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34 <option value="true">Paired</option>
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35 </param>
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36 <when value="true">
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37 <param name="input1" type="data" format="fasta,fastq" label="Input reads (mate 1)"/>
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38 <param name="input2" type="data" format="fasta,fastq" label="Input reads (mate 2)"/>
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39 </when>
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40 <when value="">
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41 <param name="input1" type="data" format="fasta,fastq" label="Input reads"/>
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42 </when>
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43 </conditional>
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44 <param name="bases" type="text" value="N" label="Bases to filter on"/>
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45 <param name="thres" type="float" value="0.5" min="0" max="1" label="Frequency threshold" help="Trim when the frequency of filter bases (or non-filter bases, if inverting) exceeds this value."/>
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46 <param name="win_len" type="integer" value="10" min="1" label="Size of the window"/>
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47 <param name="invert" type="boolean" truevalue="--invert" falsevalue="" checked="False" label="Invert filter bases" help="Trim when the frequency of bases NOT in the &quot;filter bases&quot; list exceeds the threshold."/>
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48 <conditional name="min_len">
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49 <param name="has_min_len" type="boolean" truevalue="true" falsevalue="" checked="False" label="Set a minimum read length"/>
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50 <when value="true">
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51 <param name="value" type="integer" value="10" min="0" label="Minimum read length" help="Reads trimmed to less than this length will be omitted from the output. Pairs will be preserved: both must exceed this threshold to be kept."/>
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52 </when>
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53 </conditional>
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54 </inputs>
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55 <outputs>
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56 <data name="output1" format_source="input1" label="$tool.name on $on_string"/>
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57 <data name="output2" format_source="input2" label="$tool.name on $on_string (mate 2)">
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58 <filter>paired['is_paired']</filter>
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59 </data>
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60 </outputs>
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61
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62 <help>
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63
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64 .. class:: infomark
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65
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66 **What it does**
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67
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68 This tool trims the 3' ends of reads based on the presence of the given bases. For instance, trim when N's are encountered or when the GC content exceeds a certain frequency.
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69
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70
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71 .. class:: infomark
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72
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73 **How it works**
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74
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75 This will slide along the read with a window, and trim once the frequency of filter bases exceeds the frequency threshold (unless "Invert filter bases" is enabled, in which case it will trim once non-filter bases exceed the threshold).
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76
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77 The trim point will be just before the first (leftmost) filter base in the final window (the one where the frequency exceeded the threshold).
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78
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79
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80 .. class:: infomark
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81
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82 **Input**
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83
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84 The inputs can be in the following formats: fasta, fastq, fastqsanger, fastqillumina, and fastqsolexa. Both must be either a fasta or fastq type (no mixing fastq and fasta).
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85
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86 </help>
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87
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88 </tool>