Mercurial > repos > iuc > dada2_filterandtrim

annotate dada2_filterAndTrim.xml @ 9:e8fba04706d3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 9bbc0898b9bbe73c7fc60ac162d80d749a7f97c1
author iuc
date Fri, 24 May 2024 11:41:31 +0000
parents 7434cc396c7b
children
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cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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1 <tool id="dada2_filterAndTrim" name="dada2: filterAndTrim" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
cc41546adf56 "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>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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3 <macros>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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4 <import>macros.xml</import>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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5 </macros>
6
34e55239e68b 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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cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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7 <expand macro="requirements"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
cc41546adf56 "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[
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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11 Rscript '$dada2_script'
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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12 ]]></command>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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13 <configfiles>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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14 <configfile name="dada2_script"><![CDATA[
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34e55239e68b 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"
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16 #set $compress_output = str($paired_cond.reads.forward.ext.endswith('gz')).upper()
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iuc
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17 #else
34e55239e68b 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()
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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19 #end if
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cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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20 truncQ <- c($trim.truncQ)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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21 truncLen <- c($trim.truncLen)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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22 trimLeft <- c($trim.trimLeft)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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23 trimRight <- c($trim.trimRight)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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24 #if str($filter.maxLen) == ""
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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25 maxLen <- c(Inf)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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26 #else:
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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27 maxLen <- c($filter.maxLen)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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28 #end if
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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29 minLen <- c($filter.minLen)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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30 maxN <- c($filter.maxN)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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31 minQ <- c($filter.minQ)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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32 #if str($filter.maxEE) == ""
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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33 maxEE <- c(Inf)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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34 #else:
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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35 maxEE <- c($filter.maxEE)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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36 #end if
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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37 #if $paired_cond.paired_select != "single" and $seprev_cond.seprev_select == "yes"
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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38 truncQ <- c(truncQ,$seprev_cond.trim.truncQ)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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39 truncLen <- c(truncLen,$seprev_cond.trim.truncLen)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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40 trimLeft <- c(trimLeft,$seprev_cond.trim.trimLeft)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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41 trimRight <- c(trimRight,$seprev_cond.trim.trimRight)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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42 #if str($seprev_cond.filter.maxLen) == ""
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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43 maxLen <- c(maxLen,Inf)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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44 #else:
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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45 maxLen <- c(maxLen,$seprev_cond.filter.maxLen)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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46 #end if
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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47 minLen <- c(minLen,$seprev_cond.filter.minLen)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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48 maxN <- c(maxN,$seprev_cond.filter.maxN)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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49 minQ <- c(minQ,$seprev_cond.filter.minQ)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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50 #if str($seprev_cond.filter.maxEE) == ""
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51 maxEE <- c(maxEE,Inf)
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52 #else:
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53 maxEE <- c(maxEE,$seprev_cond.filter.maxEE)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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54 #end if
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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55 #end if
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56
cc41546adf56 "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
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60 filt.rev <- NULL
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61 #if $paired_cond.paired_select == "paired"
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62 fwd <- c(fwd, '$paired_cond.reads.forward')
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63 rev <- c(rev, '$paired_cond.reads.reverse')
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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64 filt.fwd <- c(filt.fwd, '$paired_output.forward')
cc41546adf56 "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')
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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66 #else if $paired_cond.paired_select == "separate"
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67 fwd <- c(fwd, '$paired_cond.reads')
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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68 rev <- c(rev, '$paired_cond.sdaer')
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69 filt.fwd <- c(filt.fwd, '$output_fwd')
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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70 filt.rev <- c(filt.rev, '$output_rev')
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71 #else
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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72 fwd <- c(fwd, '$paired_cond.reads')
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73 filt.fwd <- c(filt.fwd, '$output_single')
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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74 #end if
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75
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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76 #if str($orientFwd) == ""
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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77 orientFwd <- NULL
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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78 #else
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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79 orientFwd <- "$orientFwd"
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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80 #end if
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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81
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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82 library(dada2, quietly=T)
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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83
6
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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84 ftout <- filterAndTrim(fwd, filt.fwd, rev, filt.rev, compress = $compress_output,
0
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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85 truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen,
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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86 minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.lowcomplex = $rmlowcomplex,
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87 rm.phix = $rmPhiX, orient.fwd = orientFwd)
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88
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89 rownames(ftout) <- c( '$paired_cond.reads.element_identifier' )
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90 write.table(ftout, "$outtab", quote=F, sep="\t", col.names=NA)
2
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91
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92 if(0 %in% ftout){
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93 quit(save="no", status="1")
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94 }
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95
0
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96 ]]></configfile>
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97 </configfiles>
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98 <inputs>
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99 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fwd" argument_rev="rev"/>
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100 <expand macro="trimmers"/>
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101 <expand macro="filters"/>
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102 <conditional name="seprev_cond">
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103 <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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104 <option value="no">no</option>
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105 <option value="yes">yes</option>
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106 </param>
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107 <when value="no"/>
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108 <when value="yes">
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109 <expand macro="trimmers"/>
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110 <expand macro="filters"/>
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111 </when>
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112 </conditional>
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113 <param argument="rmPhiX" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Discard reads matching the PhiX genome" />
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114 <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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115 <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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116 <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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117 </inputs>
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118 <outputs>
6
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119 <collection name="paired_output" type="paired" format_source="reads['forward']" label="${tool.name} on ${on_string}: Paired reads" >
0
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120 <filter>paired_cond['paired_select'] == "paired"</filter>
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121 </collection>
8
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122 <data name="output_single" format_source="paired_cond|reads" label="${tool.name} on ${on_string}: Reads" >
0
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123 <filter>paired_cond['paired_select'] == "single"</filter>
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124 </data>
8
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125 <data name="output_fwd" format_source="paired_cond|reads" default_identifier_source="paired_cond|reads" label="${tool.name} on ${on_string}: Forward reads" >
0
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126 <filter>paired_cond['paired_select'] == "separate"</filter>
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127 </data>
8
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128 <data name="output_rev" format_source="paired_cond|sdaer" default_identifier_source="paired_cond|sdaer" label="${tool.name} on ${on_string}: Reverse reads" >
0
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129 <filter>paired_cond['paired_select'] == "separate"</filter>
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130 </data>
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131 <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
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132 <filter>output_statistics</filter>
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133 </data>
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134 </outputs>
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135 <tests>
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136 <!-- paired data in paired collection -->
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137 <test expect_num_outputs="4">
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138 <conditional name="paired_cond">
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139 <param name="paired_select" value="paired"/>
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140 <param name="reads">
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141 <collection type="paired">
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142 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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143 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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144 </collection>
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145 </param>
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146 </conditional>
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147 <output_collection name="paired_output" type="paired" count="2">
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148 <element name="forward" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
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149 <element name="reverse" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
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150 </output_collection>
2
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151 <!-- 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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152 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular" lines_diff="2">
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153 <assert_contents>
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154 <has_text text="745" />
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155 <has_text text="750" />
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156 </assert_contents>
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157 </output>
0
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158 </test>
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159 <!-- paired data given separately -->
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160 <test expect_num_outputs="3">
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161 <conditional name="paired_cond">
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162 <param name="paired_select" value="separate"/>
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163 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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164 <param name="sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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165 </conditional>
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166 <output name="output_fwd" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
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167 <output name="output_rev" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
2
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168 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular"/>
0
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169 </test>
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diff changeset
170 <!-- single end data -->
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
171 <test expect_num_outputs="1">
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
172 <conditional name="paired_cond">
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
173 <param name="paired_select" value="single"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
174 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
175 </conditional>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
176 <param name="rmPhiX" value="TRUE" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
177 <param name="rmlowcomplex" value="2" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
178 <param name="orientFwd" value="TACGG" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
179 <param name="output_statistics" value="FALSE" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
180 <output name="output_fwd" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
181 </test>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
182 <!-- single end data trimming -->
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
183 <test expect_num_outputs="1">
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
184 <conditional name="paired_cond">
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
185 <param name="paired_select" value="single"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
186 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
187 </conditional>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
188 <param name="trim|truncQ" value="30" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
189 <param name="trim|trimLeft" value="150" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
190 <param name="trim|trimRight" value="2" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
191 <param name="trim|truncLen" value="2" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
192 <param name="output_statistics" value="FALSE" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
193 <output name="output_fwd" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
194 </test>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
195 <!-- single end data filtering -->
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
196 <test expect_num_outputs="1">
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
197 <conditional name="paired_cond">
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
198 <param name="paired_select" value="single"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
199 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
200 </conditional>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
201 <param name="filter|maxLen" value="255" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
202 <param name="filter|minLen" value="60" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
203 <param name="filter|maxN" value="100" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
204 <param name="filter|minQ" value="13" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
205 <param name="filter|maxEE" value="1" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
206 <param name="output_statistics" value="FALSE" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
207 <output name="output_fwd" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
208 </test>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
209 <!-- paired data w separate filters and trimmers for reverse -->
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
210 <test expect_num_outputs="3">
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
211 <conditional name="paired_cond" >
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
212 <param name="paired_select" value="paired"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
213 <param name="reads">
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
214 <collection type="paired">
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
215 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
216 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
217 </collection>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
218 </param>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
219 </conditional>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
220 <param name="seprev_cond|seprev_select" value="yes"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
221 <param name="seprev_cond|trim|truncQ" value="30" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
222 <param name="seprev_cond|trim|trimLeft" value="150" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
223 <param name="seprev_cond|trim|trimRight" value="2" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
224 <param name="seprev_cond|trim|truncLen" value="2" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
225 <param name="seprev_cond|filter|maxLen" value="255" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
226 <param name="seprev_cond|filter|minLen" value="60" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
227 <param name="seprev_cond|filter|maxN" value="100" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
228 <param name="seprev_cond|filter|minQ" value="13" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
229 <param name="seprev_cond|filter|maxEE" value="1" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
230 <param name="output_statistics" value="FALSE" />
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
231 <output_collection name="paired_output" type="paired" count="2"/>
cc41546adf56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
232 </test>
6
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
233 <!-- paired data in paired collection with uncompressed input -->
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
234 <test expect_num_outputs="4">
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
235 <conditional name="paired_cond">
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
236 <param name="paired_select" value="paired"/>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
237 <param name="reads">
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
238 <collection type="paired">
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
239 <element name="forward" value="F3D0_S188_L001_R1_001.fastq" ftype="fastqsanger"/>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
240 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq" ftype="fastqsanger"/>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
241 </collection>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
242 </param>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
243 </conditional>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
244 <output_collection name="paired_output" type="paired" count="2">
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
245 <element name="forward" value="filterAndTrim_F3D0_R1.fq" ftype="fastqsanger" />
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
246 <element name="reverse" value="filterAndTrim_F3D0_R2.fq" ftype="fastqsanger" />
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
247 </output_collection>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
248 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular" lines_diff="2">
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
249 <assert_contents>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
250 <has_text text="745" />
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
251 <has_text text="750" />
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
252 </assert_contents>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
253 </output>
34e55239e68b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents: 2
diff changeset
254 </test>
2
23fc35093b11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
255
23fc35093b11 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
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256 <!-- test failure in case all reads are filtered -->
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257 <test expect_exit_code="1" expect_failure="true">
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258 <conditional name="paired_cond" >
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259 <param name="paired_select" value="paired"/>
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260 <param name="reads">
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261 <collection type="paired">
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262 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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263 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
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264 </collection>
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265 </param>
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266 </conditional>
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267 <param name="filter|minLen" value="1000" />
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268 <param name="output_statistics" value="FALSE" />
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269 </test>
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270
0
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271 </tests>
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272
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273 <help><![CDATA[
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274 Description
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275 ...........
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276
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277 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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278
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279 Usage
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280 .....
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281
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282 **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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283
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284 **Output** is a (paired) collection of filtered and trimmed paired FASTQ datasets (again one data set or pair per sample).
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285
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286 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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287
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288 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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289
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290 Details
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291 .......
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292
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293 *Trimming and filtering*:
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294
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295 - Truncation of the read length is enforced after trimming of the right end.
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296 - The long read filter is applied before trimming and the short read filter after trimming.
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297 - For details on the calculation of the number of expected errors see also https://doi.org/10.1093/bioinformatics/btv401
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298
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299
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300 *String present at the start of valid reads* (orient.fwd):
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301
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302 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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303
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304 *Low complexity filter kmer threshold"*
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305
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306 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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307
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308 Notes
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309 .....
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310
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311 This step may be replaced by alternative tools to filter and trim short read data if the following is ensured:
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312
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313 - For paired end data unpaired reads must be removed.
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314 - There must not be a read containing a non-canonical nucleotide (N).
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315
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316 @HELP_OVERVIEW@
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317 ]]></help>
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318 <expand macro="citations"/>
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319 </tool>