Mercurial > repos > iuc > mothur_trim_seqs

annotate trim.seqs.xml @ 12:8c4958711551 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 22:46:36 +0000
parents 4929eb3e0037
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_trim_seqs" name="Trim.seqs" version="@WRAPPER_VERSION@.0">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Trim sequences - primers, barcodes, quality</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
1
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
1
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
e695fda56931 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$fasta' fasta.dat &&
e695fda56931 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$names' names.dat &&
e695fda56931 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s '$count' count.dat &&
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16 #if $oligo.add == "yes":
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17 ln -s '$oligo.oligos' oligo.oligos.dat &&
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18 #end if
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19 #if $qual.add2 == "yes":
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20 ln -s '$qual.qfile' qual.qfile.dat &&
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21 #end if
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22
3
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23 echo 'trim.seqs(
e695fda56931 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 fasta=fasta.dat,
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25 minlength=$minlength,
e695fda56931 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 maxlength=$maxlength,
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27 maxambig=$maxambig,
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28 maxhomop=$maxhomop,
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29 keepfirst=$keepfirst,
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30 removelast=$removelast,
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31 #if $oligo.add == "yes":
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32 oligos=oligo.oligos.dat,
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33 bdiffs=$oligo.bdiffs,
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34 pdiffs=$oligo.pdiffs,
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35 tdiffs=$oligo.tdiffs,
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36 ldiffs=$oligo.ldiffs,
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37 sdiffs=$oligo.sdiffs,
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38 keepforward=$oligo.keepforward,
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39 allfiles=$oligo.allfiles,
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40 #end if
e695fda56931 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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41 #if $qual.add2 == "yes":
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42 qfile=qual.qfile.dat,
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43 qaverage=$qual.qaverage,
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44 qthreshold=$qual.qthreshold,
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45 qwindowaverage=$qual.qwindowaverage,
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46 qwindowsize=$qual.qwindowsize,
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47 rollaverage=$qual.rollaverage,
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48 qstepsize=$qual.qstepsize,
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49 qtrim=$qual.qtrim,
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50 #end if
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51 flip=$flip,
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52 #if $names:
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53 name=names.dat,
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54 #end if
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55 logtransform=$logtransform,
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56 checkorient=$checkorient,
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57 #if $count:
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58 count=count.dat,
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59 #end if
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60 processors='\${GALAXY_SLOTS:-8}'
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61 )'
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62 | sed 's/ //g' ## mothur trips over whitespace
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63 | mothur
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64 | tee mothur.out.log
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65
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66 ## prevent these two files from being gathered into collection
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67 && mv fasta.trim.fasta fasta.trim
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68 && mv fasta.scrap.fasta fasta.scrap
0
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69 ]]></command>
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70 <inputs>
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71 <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/>
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72 <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
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73 <param name="minlength" type="integer" value="0" min="0" label="minlength - Minimum Sequence Length (default 0, ignored if &#060; 1 )"/>
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74 <param name="maxlength" type="integer" value="0" min="0" label="maxlength - Maximum Sequence Length (default 0, ignored if &#060; 1)"/>
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75 <param name="maxambig" type="integer" value="-1" min="-1" label="maxambig - Maximum ambiguous bases (default -1, ignored if &#060; 0)"/>
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76 <param name="maxhomop" type="integer" value="0" min="0" label="maxhomop - Maximum homopolymers (default 0, ignored if &#060; 1)"/>
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77 <param name="keepfirst" type="integer" value="0" min="0" label="keepfirst - ignored if &#060; 0)" help="trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements"/>
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78 <param name="removelast" type="integer" value="0" min="0" label="removelast - ignored if &#060; 0)" help="removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements"/>
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79 <conditional name="oligo">
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80 <param name="add" type="select" label="Trim with an oligos file?" help="">
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81 <option value="no">no</option>
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82 <option value="yes">yes</option>
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83 </param>
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84 <when value="no"/>
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85 <when value="yes">
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86 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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87 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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88 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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89 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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90 <param name="ldiffs" type="integer" value="0" min="0" optional="true" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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91 <param name="sdiffs" type="integer" value="0" min="0" optional="true" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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92 <param name="keepforward" type="boolean" truevalue="true" falsevalue="false" checked="false" label="keepforward - keep the primer"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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93 <param name="allfiles" type="boolean" truevalue="true" falsevalue="false" checked="false" label="allfiles - separate into file per barcode"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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94 </when>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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95 </conditional>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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96 <conditional name="qual">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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97 <param name="add2" type="select" label="Trim based on a quality file?" help="">
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98 <option value="no">no</option>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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99 <option value="yes">yes</option>
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100 </param>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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101 <when value="no"/>
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102 <when value="yes">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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103 <param name="qfile" type="data" format="qual454" label="qfile - 454 quality file"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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104 <param name="qaverage" type="integer" value="0" min="0" label="qaverage - remove sequences that have an average base quality below this value (ignored if &#060; 1)"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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105 <param name="qthreshold" type="integer" value="0" min="0" label="qthreshold - remove sequences that have any base quality below this value (ignored if &#060; 1)"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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106 <param name="qwindowaverage" type="integer" value="0" min="0" label="qwindowaverage - remove sequences that have an average base quality below this value over a window (ignored if &#060; 1)"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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107 <param name="qwindowsize" type="integer" value="50" min="0" label="qwindowsize - number of bases in a window. Default=50."/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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108 <param name="rollaverage" type="integer" value="0" min="0" label="rollaverage - remove sequences that have an average base quality below this value in a rolling window (ignored if &#060; 1)"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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109 <param name="qstepsize" type="integer" value="1" min="0" label="qstepsize - number of bases to move the window over. Default=1."/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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110 <param name="qtrim" type="boolean" truevalue="true" falsevalue="false" checked="false" label="qtrim - trim sequences below qthreshold and put in trim output, else put in scrap "/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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111 </when>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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112 </conditional>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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113 <param name="flip" type="boolean" truevalue="true" falsevalue="false" checked="false" label="flip - reverse complement the trimmed sequences"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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114 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. If you run trim.seqs with an oligos file that contains group labels, trim.seqs will create a new *.trim.count_table with the group information included. "/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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115 <param name="logtransform" type="boolean" truevalue="true" falsevalue="false" checked="false" label="logtransform" help="allows you to indicate you want the averages for the qwindowaverage, rollaverage and qaverage to be calculated using a logtransform."/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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116 <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - search the reverse complement?" help="If you are running the trim.seqs command with paired barcodes or primers, you can use the checkorient parameter. When checkorient=t and mothur can't find the barcodes and primers, it will search the reverse compliment. "/>
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4929eb3e0037 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
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117 <expand macro="param-savelog"/>
0
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118 </inputs>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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119 <outputs>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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120 <expand macro="logfile-output"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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121 <data name="trim_fasta" format_source="fasta" from_work_dir="fasta.trim" label="${tool.name} on ${on_string}: trim.fasta"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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122 <data name="scrap_fasta" format_source="fasta" from_work_dir="fasta.scrap" label="${tool.name} on ${on_string}: scrap.fasta"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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123 <data name="trim_names" format="mothur.names" from_work_dir="names*.trim.names" label="${tool.name} on ${on_string}: trim.names">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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124 <filter>names</filter>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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125 </data>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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126 <data name="scrap_names" format="mothur.names" from_work_dir="names*.scrap.names" label="${tool.name} on ${on_string}: scrap.names">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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127 <filter>names</filter>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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128 </data>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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129 <data name="trim_count" format="mothur.count_table" from_work_dir="count*.trim.count_table" label="${tool.name} on ${on_string}: trim.count">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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130 <filter>count</filter>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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131 </data>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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132 <data name="scrap_count" format="mothur.count_table" from_work_dir="count*.scrap.count_table" label="${tool.name} on ${on_string}: scrap.count">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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133 <filter>count</filter>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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134 </data>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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135 <data name="trim_qual" format_source="qfile" from_work_dir="fasta*.trim.qual" label="${tool.name} on ${on_string}: trim.qual">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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136 <filter>qual['add2'] == 'yes'</filter>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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137 </data>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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138 <data name="scrap_qual" format_source="qfile" from_work_dir="fasta*.scrap.qual" label="${tool.name} on ${on_string}: scrap.qual">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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139 <filter>qual['add2'] == 'yes'</filter>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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140 </data>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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141 <data name="groups_file" format="mothur.groups" from_work_dir="fasta.groups" label="${tool.name} on ${on_string}: groups">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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142 <filter>oligo['add'] == 'yes'</filter>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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143 </data>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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144 <collection name="fasta_allfiles" type="list" label="${tool.name} on ${on_string}: allfiles fasta">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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145 <filter>oligo['add'] == 'yes' and oligo['allfiles']</filter>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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146 <discover_datasets pattern="fasta.*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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147 </collection>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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148 <collection name="groups_allfiles" type="list" label="${tool.name} on ${on_string}: allfiles groups)">
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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149 <filter>oligo['add'] == 'yes' and oligo['allfiles']</filter>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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150 <discover_datasets pattern="fasta.*?\.(?P&lt;designation&gt;.*)\.groups" format="mothur.groups"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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151 </collection>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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152 </outputs>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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153 <tests>
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154 <test><!-- test with fasta and names -->
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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155 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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156 <param name="names" value="amazon1.names" ftype="mothur.names"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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157 <param name="maxhomop" value="4"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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158 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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159 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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160 <output name="trim_names" md5="1b8c6c47052bb69524ef56ebb764fb8f" ftype="mothur.names"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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161 <output name="scrap_names" md5="80f9252837e4b189f06ec00469b88e85" ftype="mothur.names"/>
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4929eb3e0037 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
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162 <param name="savelog" value="true"/>
0
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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163 <expand macro="logfile-test"/>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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164 </test>
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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165 <test><!-- test with count table -->
47923befeb9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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166 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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167 <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
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168 <param name="maxhomop" value="4"/>
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169 <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
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170 <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
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171 <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/>
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172 <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/>
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173 <param name="savelog" value="true"/>
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174 <expand macro="logfile-test"/>
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175 </test>
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176 <test><!-- test with oligos -->
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177 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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178 <param name="add" value="yes"/>
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179 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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180 <param name="bdiffs" value="100"/>
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181 <param name="pdiffs" value="100"/>
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182 <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
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183 <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
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184 <output name="groups_file" md5="198957282c234e825414e175d926046a" ftype="mothur.groups"/>
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185 <param name="savelog" value="true"/>
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186 <expand macro="logfile-test"/>
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187 </test>
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188 <test><!-- test with oligos and allfiles parameter -->
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189 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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190 <param name="add" value="yes"/>
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191 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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192 <param name="bdiffs" value="100"/>
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193 <param name="pdiffs" value="100"/>
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194 <param name="allfiles" value="true"/>
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195 <output name="trim_fasta" md5="75a8a3ae2d1fe1ff2b860480b84e9bd6" ftype="fasta"/>
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196 <output name="scrap_fasta" md5="c4fd14e70ab7d1c21d238e87624829d7" ftype="fasta"/>
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197 <output_collection name="groups_allfiles" count="9">
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198 <element name="F003D144" md5="445124b06d0c9146ae353631794c8093" ftype="mothur.groups"/>
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199 </output_collection>
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200 <output_collection name="fasta_allfiles" count="9">
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201 <element name="F003D144" md5="025ff271ac24ecb898863d7fcbfabf10" ftype="fasta"/>
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202 </output_collection>
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203 <param name="savelog" value="true"/>
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204 <expand macro="logfile-test"/>
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205 </test>
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206 <test><!-- test with qfile-->
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207 <param name="fasta" value="Fasting_Example1.fasta" ftype="fasta"/>
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208 <param name="add2" value="yes"/>
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209 <param name="qfile" value="Fasting_Example1.qual" ftype="qual454"/>
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210 <param name="maxhomop" value="4"/>
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211 <output name="trim_fasta" md5="d02f74acd6d9fb52b04a93869bb79302" ftype="fasta"/>
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212 <output name="scrap_fasta" md5="a4d3ef3d91b4c0146ec84bb7aad3987c" ftype="fasta"/>
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213 <output name="trim_qual" md5="3d4e2d3c7dd43b90660ab9c923d9eab1" ftype="qual454"/>
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214 <output name="scrap_qual" md5="22931236d082c2b77811bbf912c1f4b1" ftype="qual454"/>
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215 <param name="savelog" value="true"/>
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216 <expand macro="logfile-test"/>
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217 </test>
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218 </tests>
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219 <help><![CDATA[
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220
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221 @MOTHUR_OVERVIEW@
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222
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223 **Command Documentation**
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224
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225 The trim.seqs_ command provides the preprocessing features needed to screen and sort pyrosequences. The command will enable you to trim off primer sequences and barcodes, use the barcode information to generate a group file and split a fasta file into sub-files, screen sequences based on the qual file that comes from 454 sequencers, cull sequences based on sequence length and the presence of ambiguous bases and get the reverse complement of your sequences. While this analysis is clearly geared towards pyrosequencing collections, it can also be used with traditional Sanger sequences.
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226
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227 .. _trim.seqs: https://www.mothur.org/wiki/Trim.seqs
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228
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229 ]]></help>
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230 <expand macro="citations"/>
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231 </tool>