Mercurial > repos > iuc > mothur_screen_seqs

annotate screen.seqs.xml @ 8:f4d7d5755f01 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"
author iuc
date Thu, 05 Nov 2020 23:12:15 +0000
parents 6202ff80199f
children c1feef4d5e34
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0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
1 <tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.0">
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>Screen sequences</description>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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3 <macros>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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5 </macros>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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6 <expand macro="requirements"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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10 @SHELL_OPTIONS@
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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12 ## create symlinks to input datasets
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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13 ln -s '$fasta' fasta.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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14 ln -s '$names' names.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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15 ln -s '$groups' groups.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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16 ln -s '$qfile' qfile.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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17 ln -s '$count' count.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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18 ln -s '$taxonomy' taxonomy.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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19 ln -s '$summary' summary.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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20 #if $contigsrep.usecontigs == "yes":
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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21 ln -s '$contigsrep.contigsreport' contigsreport.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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23 #if $alignrep.usealign == "yes":
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 ln -s '$alignrep.alignreport' alignreport.dat &&
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 #end if
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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27 echo 'screen.seqs(
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 fasta=fasta.dat
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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29 #if int($start) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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30 ,start=$start
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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32 #if int($end) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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33 ,end=$end
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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34 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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35 #if int($minlength) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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36 ,minlength=$minlength
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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37 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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38 #if int($maxlength) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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39 ,maxlength=$maxlength
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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40 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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41 #if int($maxambig) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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42 ,maxambig=$maxambig
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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43 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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44 #if int($maxhomop) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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45 ,maxhomop=$maxhomop
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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46 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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47 #if int($criteria) > -1:
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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48 ,criteria=$criteria
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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49 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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50 #if $optimize:
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51 ,optimize=$optimize
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52 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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53 #if $qfile:
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54 ,qfile=qfile.dat
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55 #end if
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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56 #if $names:
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57 ,name=names.dat
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58 #end if
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59 #if $groups:
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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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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=$contigsrep.ostart
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75 ,oend=$contigsrep.oend
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76 ,mismatches=$contigsrep.mismatches
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77 #end if
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78 #if $alignrep.usealign == "yes":
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79 ,alignreport=alignreport.dat
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80 ,minsim=$alignrep.minsim
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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81 ,minscore=$alignrep.minscore
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82 ,maxinsert=$alignrep.maxinsert
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83 #end if
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84 ,processors='"\${GALAXY_SLOTS:-8}"'
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85 )'
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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>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 <inputs>
3
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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>
3
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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>
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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"/>
3
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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 ${on_string}: qfile">
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151 <filter>qfile</filter>
0
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152 </data>
3
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153 <data name="names_out" format="mothur.names" from_work_dir="names*.good.dat" label="${tool.name} on ${on_string}: names">
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154 <filter>names</filter>
0
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155 </data>
3
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156 <data name="groups_out" format="mothur.groups" from_work_dir="groups*.good.dat" label="${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 ${on_string}: align.report">
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160 <filter>alignrep.alignreport</filter>
0
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161 </data>
3
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162 <data name="contigsreport_out" format="tabular" from_work_dir="contigsreport.good.contigs.report" label="${tool.name} on ${on_string}: contigs.report">
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163 <filter>contigsrep.contigsreport</filter>
0
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164 </data>
3
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165 <data name="count_out" format="mothur.count_table" from_work_dir="count*.good.dat" label="${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>
3
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171 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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172 <param name="maxambig" value="0"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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173 <param name="maxlength" value="275"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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174 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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175 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos" ftype="mothur.accnos"/>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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176 <param name="savelog" value="true"/>
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177 <expand macro="logfile-test"/>
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178 </test>
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179 <test><!-- test with count table -->
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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180 <param name="fasta" value="amazon.fasta" ftype="mothur.align"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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181 <param name="count" value="amazon1.count_table"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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182 <param name="maxambig" value="0"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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183 <param name="maxlength" value="500"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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184 <output name="fasta_out" ftype="mothur.align">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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185 <assert_contents>
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186 <expand macro="test-fasta-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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187 <has_text text="U68638"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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188 <not_has_text text="U68589"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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189 </assert_contents>
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190 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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191 <output name="count_out" ftype="mothur.count_table">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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192 <assert_contents>
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iuc
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193 <expand macro="test-count-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
194 <has_text text="U68638"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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195 <not_has_text text="U68589"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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196 </assert_contents>
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197 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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198 <output name="bad_accnos" ftype="mothur.accnos">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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199 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
200 <expand macro="test-accnos-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
201 <not_has_text text="U68638"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
202 <has_text text="U68589"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
203 <has_text text="ambig"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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204 <has_text text="length"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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205 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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206 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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207 <param name="savelog" value="true"/>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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208 <expand macro="logfile-test"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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209 </test>
3
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210 <test><!-- test screening with contigsreport -->
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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diff changeset
211 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta" ftype="fasta"/>
0
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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diff changeset
212 <param name="maxambig" value="0"/>
125a6ae65887 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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213 <param name="maxlength" value="275"/>
3
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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214 <param name="usecontigs" value="yes"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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215 <param name="contigsreport" value="Mock_S280_L001_R1_001_small.contigs.report"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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216 <param name="mismatches" value="18"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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diff changeset
217 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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diff changeset
218 <output name="bad_accnos" ftype="mothur.accnos">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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219 <assert_contents>
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iuc
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diff changeset
220 <expand macro="test-accnos-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
221 <has_text text="mismatches"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
222 <has_text text="ambig"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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223 </assert_contents>
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224 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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225 <output name="contigsreport_out" ftype="tabular">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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226 <assert_contents>
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iuc
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diff changeset
227 <expand macro="test-contigsreport-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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228 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_22487_4260"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
229 <has_text text="M00967_43_000000000-A3JHG_1_1101_15923_3823"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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230 </assert_contents>
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iuc
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diff changeset
231 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
232 <param name="savelog" value="true"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
233 <expand macro="logfile-test"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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234 </test>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
235 <test><!-- test screening with alignment report -->
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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diff changeset
236 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta" ftype="fasta"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
237 <param name="maxambig" value="0"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
238 <param name="maxlength" value="275"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
239 <param name="usealign" value="yes"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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240 <param name="alignreport" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align.report"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
241 <param name="minscore" value="100"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
242 <output name="fasta_out" ftype="fasta">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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diff changeset
243 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
244 <expand macro="test-fasta-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
245 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
246 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
247 </assert_contents>
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iuc
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diff changeset
248 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
249 <output name="bad_accnos" ftype="mothur.accnos">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
250 <assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
parents: 2
diff changeset
251 <expand macro="test-accnos-format"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
252 <has_text text="score"/>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
253 </assert_contents>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
254 </output>
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
iuc
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diff changeset
255 <output name="alignreport_out" ftype="mothur.align.report">
6202ff80199f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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256 <assert_contents>
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257 <expand macro="test-alignreport-format"/>
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258 <not_has_text text="M00967_43_000000000-A3JHG_1_1101_14010_4122"/>
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259 <has_text text="M00967_43_000000000-A3JHG_1_1101_19936_3208"/>
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260 </assert_contents>
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261 </output>
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262 <param name="savelog" value="true"/>
0
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263 <expand macro="logfile-test"/>
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264 </test>
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265 </tests>
3
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266 <help><![CDATA[
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267
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268 @MOTHUR_OVERVIEW@
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269
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270 **Command Documentation**
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271
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272 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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273
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274 .. _name: https://www.mothur.org/wiki/Name_file
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275 .. _group: https://www.mothur.org/wiki/Group_file
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276 .. _align.report: https://www.mothur.org/wiki/Align.seqs
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277 .. _screen.seqs: https://www.mothur.org/wiki/Screen.seqs
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278
3
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279 ]]></help>
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280 <expand macro="citations"/>
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281 </tool>