Mercurial > repos > iuc > mothur_screen_seqs

annotate screen.seqs.xml @ 12:f507c270eb78 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 22:42:21 +0000
parents 0b91839225a9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 5
diff changeset
1 <tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.1">
0
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Screen sequences</description>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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6 <expand macro="requirements"/>
1
d0190913cb6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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7 <expand macro="stdio"/>
0
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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8 <expand macro="version_command"/>
1
d0190913cb6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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9 <command><![CDATA[
4
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10 @SHELL_OPTIONS@
1
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11
4
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iuc
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12 ## create symlinks to input datasets
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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13 ln -s '$fasta' fasta.dat &&
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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14 ln -s '$names' names.dat &&
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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15 ln -s '$groups' groups.dat &&
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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16 ln -s '$qfile' qfile.dat &&
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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17 ln -s '$count' count.dat &&
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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18 ln -s '$taxonomy' taxonomy.dat &&
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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19 ln -s '$summary' summary.dat &&
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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20 #if $contigsrep.usecontigs == "yes":
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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21 ln -s '$contigsrep.contigsreport' contigsreport.dat &&
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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22 #end if
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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23 #if $alignrep.usealign == "yes":
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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24 ln -s '$alignrep.alignreport' alignreport.dat &&
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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25 #end if
0
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26
4
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iuc
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27 echo 'screen.seqs(
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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28 fasta=fasta.dat
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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29 #if int($start) > -1:
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iuc
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30 ,start=$start
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iuc
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31 #end if
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iuc
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32 #if int($end) > -1:
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33 ,end=$end
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iuc
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34 #end if
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iuc
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35 #if int($minlength) > -1:
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iuc
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36 ,minlength=$minlength
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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37 #end if
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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38 #if int($maxlength) > -1:
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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39 ,maxlength=$maxlength
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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40 #end if
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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41 #if int($maxambig) > -1:
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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42 ,maxambig=$maxambig
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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43 #end if
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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44 #if int($maxhomop) > -1:
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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45 ,maxhomop=$maxhomop
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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46 #end if
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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47 #if int($criteria) > -1:
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48 ,criteria=$criteria
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iuc
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49 #end if
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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50 #if $optimize:
11
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
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51 ,optimize=#echo str($optimize).replace(',','-') #
4
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52 #end if
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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53 #if $qfile:
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iuc
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54 ,qfile=qfile.dat
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55 #end if
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56 #if $names:
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iuc
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57 ,name=names.dat
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iuc
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58 #end if
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iuc
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59 #if $groups:
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iuc
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60 ,group=groups.dat
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61 #end if
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62 #if $taxonomy:
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63 ,taxonomy=taxonomy.dat
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64 #end if
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65 #if $count:
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66 ,count=count.dat
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iuc
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67 #end if
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68 #if $summary:
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69 ,summary=summary.dat
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70 #end if
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71 #if $contigsrep.usecontigs == "yes":
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72 ,contigsreport=contigsreport.dat
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73 ,minoverlap=$contigsrep.minoverlap
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74 ,ostart=$contigsrep.ostart
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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75 ,oend=$contigsrep.oend
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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76 ,mismatches=$contigsrep.mismatches
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77 #end if
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78 #if $alignrep.usealign == "yes":
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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79 ,alignreport=alignreport.dat
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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80 ,minsim=$alignrep.minsim
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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81 ,minscore=$alignrep.minscore
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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82 ,maxinsert=$alignrep.maxinsert
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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83 #end if
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iuc
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84 ,processors='"\${GALAXY_SLOTS:-8}"'
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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85 )'
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iuc
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86 | sed 's/ //g' ## mothur trips over whitespace
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87 | mothur
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88 | tee mothur.out.log
0
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89 ]]></command>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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90 <inputs>
4
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91 <param argument="fasta" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/>
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92 <param argument="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
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93 <param argument="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
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94 <param argument="minlength" type="integer" value="10" label="minlength - Remove sequences shorter than (ignored when negative)"/>
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95 <param argument="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
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96 <param argument="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>
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97 <param argument="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/>
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98 <param argument="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained (ignored when negative)"/>
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99 <param argument="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters">
0
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100 <option value="start">start</option>
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101 <option value="end">end</option>
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102 <option value="minlength">minlength</option>
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103 <option value="maxlength">maxlength</option>
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104 <option value="maxambig">maxambig</option>
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105 <option value="maxhomop">maxhomop</option>
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106 </param>
4
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107 <param argument="qfile" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/>
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108 <param argument="names" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/>
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109 <param argument="groups" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/>
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110 <param argument="summary" type="data" format="mothur.summary" optional="true" label="summary file - as created by summary.seqs"
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111 help="saves processing time when screening with parameters in the summary file"/>
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112 <param argument="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
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113 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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114 <conditional name="alignrep">
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115 <param name="usealign" type="select" label="Perform screening using an alignment report?" help="An alignment report is created by the align.seqs tool.
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116 If you provide the alignment report file you can screen your sequences using the following parameters: minsim, minscore, and maxinsert">
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117 <option value="yes">Yes</option>
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118 <option value="no" selected="true">No</option>
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119 </param>
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120 <when value="yes">
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121 <param argument="alignreport" type="data" format="mothur.align.report" label="alignreport - Align Report to screen with"/>
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122 <param argument="minsim" type="integer" value="-1" min="-1" label="minsim - Minimum similarity to template sequences during alignment"/>
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123 <param argument="minscore" type="integer" value="-1" min="-1" label="minscore - Minimum search score during alignment (ignored when negative)"/>
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124 <param argument="maxinsert" type="integer" value="-1" min="-1" label="maxinsert - Maximum number of insertions during alignment (ignored when negative)"/>
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125 </when>
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126 <when value="no"/>
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127 </conditional>
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128 <conditional name="contigsrep">
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129 <param name="usecontigs" type="select" label="Perform screening using a contigsreport?" help="A contigsreport is created by the make.contigs tool.
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130 If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches">
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131 <option value="yes">Yes</option>
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132 <option value="no" selected="true">No</option>
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133 </param>
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134 <when value="yes">
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135 <param argument="contigsreport" type="data" format="tabular" label="contigsreport - Contigs Report to screen with"
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136 help="this file is created by the make.contigs command"/>
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137 <param argument="minoverlap" type="integer" value="-1" min="-1" label="minoverlap - Minimum overlap length (ignored when negative)"/>
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138 <param argument="ostart" type="integer" value="-1" min="-1" label="ostart - Position the overlap must start by (ignored when negative)"/>
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139 <param argument="oend" type="integer" value="-1" min="-1" label="oend - Position the overlap must end after (ignored when negative)"/>
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140 <param argument="mismatches" type="integer" value="-1" min="-1" label="mismatches - Maximum number of mismatches (ignored when negative)"/>
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141 </when>
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142 <when value="no"/>
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143 </conditional>
5
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144 <expand macro="param-savelog"/>
0
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145 </inputs>
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146 <outputs>
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147 <expand macro="logfile-output"/>
4
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148 <data name="fasta_out" format_source="fasta" from_work_dir="fasta*.good.dat" label="${tool.name} on ${on_string}: good.${fasta.datatype.file_ext}"/>
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149 <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/>
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150 <data name="qfile_out" format_source="qfile" from_work_dir="qfile*.good.dat" label="${tool.name} on ${on_string}: qfile">
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151 <filter>qfile</filter>
0
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152 </data>
4
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153 <data name="names_out" format="mothur.names" from_work_dir="names*.good.dat" label="${tool.name} on ${on_string}: names">
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154 <filter>names</filter>
0
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155 </data>
4
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156 <data name="groups_out" format="mothur.groups" from_work_dir="groups*.good.dat" label="${tool.name} on ${on_string}: groups">
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157 <filter>groups</filter>
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158 </data>
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159 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport.good.align.report" label="${tool.name} on ${on_string}: align.report">
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160 <filter>alignrep.alignreport</filter>
0
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161 </data>
4
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162 <data name="contigsreport_out" format="tabular" from_work_dir="contigsreport.good.contigs.report" label="${tool.name} on ${on_string}: contigs.report">
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163 <filter>contigsrep.contigsreport</filter>
0
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164 </data>
4
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165 <data name="count_out" format="mothur.count_table" from_work_dir="count*.good.dat" label="${tool.name} on ${on_string}: count">
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166 <filter>count</filter>
0
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167 </data>
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168 </outputs>
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169 <tests>
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170 <test>
4
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diff changeset
171 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
0
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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172 <param name="maxambig" value="0"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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173 <param name="maxlength" value="275"/>
1
d0190913cb6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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parents: 0
diff changeset
174 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
d0190913cb6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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parents: 0
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175 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/>
5
921ff33138df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
iuc
parents: 4
diff changeset
176 <param name="savelog" value="true"/>
0
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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177 <expand macro="logfile-test"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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178 </test>
11
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
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diff changeset
179 <test><!-- test for multiple optimize options minlenght, maxlength, maxhomop -->
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
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diff changeset
180 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
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parents: 5
diff changeset
181 <param name="criteria" value="50"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 5
diff changeset
182 <param name="optimize" value="minlength,maxlength,maxhomop"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
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parents: 5
diff changeset
183 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.minlength.maxlength.maxhomop.good.fasta" ftype="fasta"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
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184 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.minlength.maxlength.maxhomop.bad.accnos" ftype="mothur.accnos"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 5
diff changeset
185 <param name="savelog" value="true"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 5
diff changeset
186 <expand macro="logfile-test"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
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187 </test>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
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diff changeset
188 <test><!-- test for multiple optimize options end, maxambig -->
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
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diff changeset
189 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 5
diff changeset
190 <param name="criteria" value="50"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 5
diff changeset
191 <param name="optimize" value="end,maxambig"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
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diff changeset
192 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.end.maxambig.good.fasta" ftype="fasta"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 5
diff changeset
193 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.optimize.end.maxambig.bad.accnos" ftype="mothur.accnos"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 5
diff changeset
194 <param name="savelog" value="true"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
parents: 5
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195 <expand macro="logfile-test"/>
0b91839225a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
iuc
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196 </test>
4
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
197 <test><!-- test with count table -->
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
198 <param name="fasta" value="amazon.fasta" ftype="mothur.align"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
199 <param name="count" value="amazon1.count_table"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
200 <param name="maxambig" value="0"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
201 <param name="maxlength" value="500"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
202 <output name="fasta_out" ftype="mothur.align">
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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203 <assert_contents>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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204 <expand macro="test-fasta-format"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
205 <has_text text="U68638"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
206 <not_has_text text="U68589"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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207 </assert_contents>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
208 </output>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
209 <output name="count_out" ftype="mothur.count_table">
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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210 <assert_contents>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
211 <expand macro="test-count-format"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
212 <has_text text="U68638"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
213 <not_has_text text="U68589"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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214 </assert_contents>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
215 </output>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
216 <output name="bad_accnos" ftype="mothur.accnos">
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
217 <assert_contents>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
218 <expand macro="test-accnos-format"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
219 <not_has_text text="U68638"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
220 <has_text text="U68589"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
221 <has_text text="ambig"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
222 <has_text text="length"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
223 </assert_contents>
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224 </output>
5
921ff33138df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
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225 <param name="savelog" value="true"/>
4
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
226 <expand macro="logfile-test"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
227 </test>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
228 <test><!-- test screening with contigsreport -->
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
229 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
0
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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diff changeset
230 <param name="maxambig" value="0"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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diff changeset
231 <param name="maxlength" value="275"/>
4
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
232 <param name="usecontigs" value="yes"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
233 <param name="contigsreport" value="Mock_S280_L001_R1_001_small.contigs.report"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
234 <param name="mismatches" value="18"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
235 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
236 <output name="bad_accnos" ftype="mothur.accnos">
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
237 <assert_contents>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
238 <expand macro="test-accnos-format"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
239 <has_text text="mismatches"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
240 <has_text text="ambig"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
241 </assert_contents>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
242 </output>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
243 <output name="contigsreport_out" ftype="tabular">
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
244 <assert_contents>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
245 <expand macro="test-contigsreport-format"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
246 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_22487_4260"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
247 <has_text text="M00967_43_000000000-A3JHG_1_1101_15923_3823"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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diff changeset
248 </assert_contents>
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iuc
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diff changeset
249 </output>
5
921ff33138df planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
iuc
parents: 4
diff changeset
250 <param name="savelog" value="true"/>
4
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
251 <expand macro="logfile-test"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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diff changeset
252 </test>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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parents: 3
diff changeset
253 <test><!-- test screening with alignment report -->
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
parents: 3
diff changeset
254 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
2159457a4586 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
iuc
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255 <param name="maxambig" value="0"/>
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256 <param name="maxlength" value="275"/>
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257 <param name="usealign" value="yes"/>
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258 <param name="alignreport" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report"/>
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259 <param name="minscore" value="100"/>
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260 <output name="fasta_out" ftype="fasta">
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261 <assert_contents>
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262 <expand macro="test-fasta-format"/>
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263 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/>
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264 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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265 </assert_contents>
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266 </output>
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267 <output name="bad_accnos" ftype="mothur.accnos">
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268 <assert_contents>
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269 <expand macro="test-accnos-format"/>
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270 <has_text text="score"/>
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271 </assert_contents>
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272 </output>
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273 <output name="alignreport_out" ftype="mothur.align.report">
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274 <assert_contents>
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275 <expand macro="test-alignreport-format"/>
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276 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/>
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277 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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278 </assert_contents>
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279 </output>
5
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280 <param name="savelog" value="true"/>
0
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281 <expand macro="logfile-test"/>
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282 </test>
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283 </tests>
4
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284 <help><![CDATA[
0
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285
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286 @MOTHUR_OVERVIEW@
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287
1
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288 **Command Documentation**
0
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289
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290 The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file.
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291
1
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292 .. _name: https://www.mothur.org/wiki/Name_file
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293 .. _group: https://www.mothur.org/wiki/Group_file
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294 .. _align.report: https://www.mothur.org/wiki/Align.seqs
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295 .. _screen.seqs: https://www.mothur.org/wiki/Screen.seqs
0
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296
4
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297 ]]></help>
0
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298 <expand macro="citations"/>
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299 </tool>