Mercurial > repos > iuc > dada2_filterandtrim

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48
author iuc
date Sat, 20 Dec 2025 14:09:18 +0000
parents 46ca7fe29b3e
children
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46ca7fe29b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit bbbc0e71b1db299a7c7296f25ac7adcccd27fbe3
iuc
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1 <tool id="dada2_filterAndTrim" name="dada2: filterAndTrim" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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2 <description>Filter and trim short read data</description>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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3 <macros>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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4 <import>macros.xml</import>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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5 </macros>
6
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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6 <expand macro="bio_tools"/>
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c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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7 <expand macro="requirements"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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8 <expand macro="stdio"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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9 <expand macro="version_command"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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10 <command detect_errors="exit_code"><![CDATA[
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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11 Rscript '$dada2_script'
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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12 ]]></command>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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13 <configfiles>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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14 <configfile name="dada2_script"><![CDATA[
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6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
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15 #if $paired_cond.paired_select == "paired"
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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16 #set $compress_output = str($paired_cond.reads.forward.ext.endswith('gz')).upper()
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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17 #else
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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18 #set $compress_output = str($paired_cond.reads.ext.endswith('gz')).upper()
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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19 #end if
0
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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20 truncQ <- c($trim.truncQ)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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21 truncLen <- c($trim.truncLen)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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22 trimLeft <- c($trim.trimLeft)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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23 trimRight <- c($trim.trimRight)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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24 #if str($filter.maxLen) == ""
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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25 maxLen <- c(Inf)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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26 #else:
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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27 maxLen <- c($filter.maxLen)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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28 #end if
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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29 minLen <- c($filter.minLen)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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30 maxN <- c($filter.maxN)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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31 minQ <- c($filter.minQ)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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32 #if str($filter.maxEE) == ""
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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33 maxEE <- c(Inf)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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34 #else:
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35 maxEE <- c($filter.maxEE)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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36 #end if
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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37 #if $paired_cond.paired_select != "single" and $seprev_cond.seprev_select == "yes"
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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38 truncQ <- c(truncQ,$seprev_cond.trim.truncQ)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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39 truncLen <- c(truncLen,$seprev_cond.trim.truncLen)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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40 trimLeft <- c(trimLeft,$seprev_cond.trim.trimLeft)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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41 trimRight <- c(trimRight,$seprev_cond.trim.trimRight)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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42 #if str($seprev_cond.filter.maxLen) == ""
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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43 maxLen <- c(maxLen,Inf)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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44 #else:
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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45 maxLen <- c(maxLen,$seprev_cond.filter.maxLen)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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46 #end if
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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47 minLen <- c(minLen,$seprev_cond.filter.minLen)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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48 maxN <- c(maxN,$seprev_cond.filter.maxN)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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49 minQ <- c(minQ,$seprev_cond.filter.minQ)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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50 #if str($seprev_cond.filter.maxEE) == ""
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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51 maxEE <- c(maxEE,Inf)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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52 #else:
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53 maxEE <- c(maxEE,$seprev_cond.filter.maxEE)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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54 #end if
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55 #end if
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56
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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57 fwd <- NULL
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58 rev <- NULL
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59 filt.fwd <- NULL
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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60 filt.rev <- NULL
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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61 #if $paired_cond.paired_select == "paired"
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62 fwd <- c(fwd, '$paired_cond.reads.forward')
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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63 rev <- c(rev, '$paired_cond.reads.reverse')
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64 filt.fwd <- c(filt.fwd, '$paired_output.forward')
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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65 filt.rev <- c(filt.rev, '$paired_output.reverse')
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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66 #else
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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67 fwd <- c(fwd, '$paired_cond.reads')
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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68 filt.fwd <- c(filt.fwd, '$output_single')
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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69 #end if
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70
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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71 #if str($orientFwd) == ""
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72 orientFwd <- NULL
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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73 #else
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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74 orientFwd <- "$orientFwd"
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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75 #end if
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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76
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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77 library(dada2, quietly=T)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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78
6
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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79 ftout <- filterAndTrim(fwd, filt.fwd, rev, filt.rev, compress = $compress_output,
0
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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80 truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen,
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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81 minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.lowcomplex = $rmlowcomplex,
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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82 rm.phix = $rmPhiX, orient.fwd = orientFwd)
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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83
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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84 rownames(ftout) <- c( '$paired_cond.reads.element_identifier' )
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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85 write.table(ftout, "$outtab", quote=F, sep="\t", col.names=NA)
2
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86
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87 if(0 %in% ftout){
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88 quit(save="no", status="1")
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89 }
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90
0
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91 ]]></configfile>
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92 </configfiles>
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93 <inputs>
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94 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fwd" argument_rev="rev"/>
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95 <expand macro="trimmers"/>
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96 <expand macro="filters"/>
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97 <conditional name="seprev_cond">
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98 <param name="seprev_select" type="select" label="Separate filters and trimmers for reverse reads" help="only applies to paired end data">
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99 <option value="no">no</option>
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100 <option value="yes">yes</option>
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101 </param>
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102 <when value="no"/>
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103 <when value="yes">
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104 <expand macro="trimmers"/>
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105 <expand macro="filters"/>
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106 </when>
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107 </conditional>
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108 <param argument="rmPhiX" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Discard reads matching the PhiX genome" />
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109 <param name="rmlowcomplex" argument="rm.lowcomplex" type="integer" value="0" min="0" label="Low complexity filter kmer threshold" help="see below"/>
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110 <param name="orientFwd" argument="orient.fwd" type="text" value="" optional="true" label="String present at the start of valid reads" help="see below"/>
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111 <param name="output_statistics" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Output statistics" help="Create extra table with the number of reads pre and post filtering" />
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112 </inputs>
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113 <outputs>
6
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114 <collection name="paired_output" type="paired" format_source="reads['forward']" label="${tool.name} on ${on_string}: Paired reads" >
0
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115 <filter>paired_cond['paired_select'] == "paired"</filter>
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116 </collection>
8
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117 <data name="output_single" format_source="paired_cond|reads" label="${tool.name} on ${on_string}: Reads" >
0
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118 <filter>paired_cond['paired_select'] == "single"</filter>
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119 </data>
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120 <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
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121 <filter>output_statistics</filter>
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122 </data>
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123 </outputs>
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124 <tests>
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125 <!-- paired data in paired collection -->
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126 <test expect_num_outputs="4">
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127 <conditional name="paired_cond">
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128 <param name="paired_select" value="paired"/>
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129 <param name="reads">
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130 <collection type="paired">
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131 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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132 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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133 </collection>
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134 </param>
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135 </conditional>
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136 <output_collection name="paired_output" type="paired" count="2">
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137 <element name="forward" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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138 <element name="reverse" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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139 </output_collection>
2
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140 <!-- in the test the used collection (the pair) has the name "Unnamed collection" hence we have two lines difference. In the real world the pair will have the sample name, i.e its OK. To be sure we test for the counts as well -->
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141 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular" lines_diff="2">
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142 <assert_contents>
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143 <has_text text="745" />
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144 <has_text text="750" />
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145 </assert_contents>
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146 </output>
0
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147 </test>
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148 <!-- single end data -->
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149 <test expect_num_outputs="1">
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150 <conditional name="paired_cond">
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151 <param name="paired_select" value="single"/>
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152 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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153 </conditional>
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154 <param name="rmPhiX" value="TRUE" />
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155 <param name="rmlowcomplex" value="2" />
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156 <param name="orientFwd" value="TACGG" />
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157 <param name="output_statistics" value="FALSE" />
10
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158 <output name="output_single" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
0
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159 </test>
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160 <!-- single end data trimming -->
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161 <test expect_num_outputs="1">
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162 <conditional name="paired_cond">
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163 <param name="paired_select" value="single"/>
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164 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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165 </conditional>
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166 <param name="trim|truncQ" value="30" />
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167 <param name="trim|trimLeft" value="150" />
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168 <param name="trim|trimRight" value="2" />
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parents:
diff changeset
169 <param name="trim|truncLen" value="2" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
170 <param name="output_statistics" value="FALSE" />
10
3efaa80a3e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48
iuc
parents: 9
diff changeset
171 <output name="output_single" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
0
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
172 </test>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
173 <!-- single end data filtering -->
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
174 <test expect_num_outputs="1">
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
175 <conditional name="paired_cond">
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
176 <param name="paired_select" value="single"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
177 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
178 </conditional>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
179 <param name="filter|maxLen" value="255" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
180 <param name="filter|minLen" value="60" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
181 <param name="filter|maxN" value="100" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
182 <param name="filter|minQ" value="13" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
183 <param name="filter|maxEE" value="1" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
184 <param name="output_statistics" value="FALSE" />
10
3efaa80a3e20 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48
iuc
parents: 9
diff changeset
185 <output name="output_single" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
0
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
186 </test>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
187 <!-- paired data w separate filters and trimmers for reverse -->
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
188 <test expect_num_outputs="3">
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
189 <conditional name="paired_cond" >
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
190 <param name="paired_select" value="paired"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
191 <param name="reads">
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
192 <collection type="paired">
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
193 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
194 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
195 </collection>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
196 </param>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
197 </conditional>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
198 <param name="seprev_cond|seprev_select" value="yes"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
199 <param name="seprev_cond|trim|truncQ" value="30" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
200 <param name="seprev_cond|trim|trimLeft" value="150" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
201 <param name="seprev_cond|trim|trimRight" value="2" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
202 <param name="seprev_cond|trim|truncLen" value="2" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
203 <param name="seprev_cond|filter|maxLen" value="255" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
204 <param name="seprev_cond|filter|minLen" value="60" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
205 <param name="seprev_cond|filter|maxN" value="100" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
206 <param name="seprev_cond|filter|minQ" value="13" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
207 <param name="seprev_cond|filter|maxEE" value="1" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
208 <param name="output_statistics" value="FALSE" />
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
209 <output_collection name="paired_output" type="paired" count="2"/>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
210 </test>
6
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
211 <!-- paired data in paired collection with uncompressed input -->
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
212 <test expect_num_outputs="4">
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
213 <conditional name="paired_cond">
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
214 <param name="paired_select" value="paired"/>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
215 <param name="reads">
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
216 <collection type="paired">
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
217 <element name="forward" value="F3D0_S188_L001_R1_001.fastq" ftype="fastqsanger"/>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
218 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq" ftype="fastqsanger"/>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
219 </collection>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
220 </param>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
221 </conditional>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
222 <output_collection name="paired_output" type="paired" count="2">
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
223 <element name="forward" value="filterAndTrim_F3D0_R1.fq" ftype="fastqsanger" />
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
224 <element name="reverse" value="filterAndTrim_F3D0_R2.fq" ftype="fastqsanger" />
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
225 </output_collection>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
226 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular" lines_diff="2">
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
227 <assert_contents>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
228 <has_text text="745" />
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
229 <has_text text="750" />
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
230 </assert_contents>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
231 </output>
6fa489a54ae8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 5
diff changeset
232 </test>
2
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
233
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
234 <!-- test failure in case all reads are filtered -->
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
235 <test expect_exit_code="1" expect_failure="true">
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
236 <conditional name="paired_cond" >
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
237 <param name="paired_select" value="paired"/>
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
238 <param name="reads">
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
239 <collection type="paired">
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
240 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
241 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
242 </collection>
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
243 </param>
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
244 </conditional>
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
245 <param name="filter|minLen" value="1000" />
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
246 <param name="output_statistics" value="FALSE" />
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
247 </test>
3830850e1ad7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
248
0
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
249 </tests>
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
250
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
251 <help><![CDATA[
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
252 Description
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
253 ...........
c6d04ca05d18 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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254
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255 Filters and trims a FASTQ dataset (can be compressed) based on several user-definable criteria, and outputs a compressed FASTQ data set containing those trimmed reads which passed the filters. For paired end data forward and reverse FASTQ datasets can be provided as pair of FASTQ datasets (or two separate data sets), in which case filtering is performed on the forward and reverse reads independently, and both reads must pass for the read pair to be in the output.
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256
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257 Usage
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258 .....
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259
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260 **Input** is a FASTQ dataset (or a pair in case of paired end data) containing all reads of a sample. It is suggested to organize them in a (paired) collection (in particular if you have multiple samples).
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261
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262 **Output** is a (paired) collection of filtered and trimmed paired FASTQ datasets (again one data set or pair per sample).
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263
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264 Upstream dada2 tools are *dada2: learnErrorRates* and *dada2: dada*. Note that these tools do not work on paired end data. So, if you have paired end data you need to split the generated paired collection into one containing the forward reads and one containing the reverse reads. This can be done by the *unzip collection* tool.
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265
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266 An additional tabular output gives the number of reads before and after trimming. This can data set can be used as input for *dada2: sequence counts* to track the sequence counts for each sample through all dada2 pipeline step.
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267
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268 Details
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269 .......
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270
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271 *Trimming and filtering*:
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272
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273 - Truncation of the read length is enforced after trimming of the right end.
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274 - The long read filter is applied before trimming and the short read filter after trimming.
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275 - For details on the calculation of the number of expected errors see also Calahan et al. 2016
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276
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277 *String present at the start of valid reads* (orient.fwd):
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278
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279 This string is compared to the start of each read, and the reverse complement of each read. If it exactly matches the start of the read, the read is kept. If it exactly matches the start of the reverse complement read, the read is reverse-complemented and kept. Otherwise the read if filtered out. For paired reads, the string is compared to the start of the forward and reverse reads, and if it matches the start of the reverse read the reads are swapped and kept. The primary use of this parameter is to unify the orientation of amplicon sequencing libraries that are a mixture of forward and reverse orientations, and that include the forward primer on the reads.
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280
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281 *Low complexity filter kmer threshold"*
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282
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283 If greater than 0, reads with an effective number of kmers less than this value will be removed. The effective number of kmers is determined as a Shannon information approximation. The default kmer-size is 2, and therefore perfectly random sequences will approachan effective kmer number of 16 = 4 (nucleotides) ^ 2 (kmer size).
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284
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285 Notes
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286 .....
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287
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288 This step may be replaced by alternative tools to filter and trim short read data if the following is ensured:
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289
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290 - For paired end data unpaired reads must be removed.
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291 - There must not be a read containing a non-canonical nucleotide (N).
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292
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293 @HELP_OVERVIEW@
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294 ]]></help>
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295 <expand macro="citations"/>
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296 </tool>