Mercurial > repos > iuc > mothur_get_seqs

annotate get.seqs.xml @ 0:bfd467665e6c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:44:07 -0400
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children 5acd4d7339b9
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0
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_get_seqs" name="Get.seqs" version="@WRAPPER_VERSION@.0">
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Picks sequences by name</description>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
bfd467665e6c 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"/>
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9 <command><![CDATA[
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$accnos" accnos.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$fasta_in" fasta_in.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ln -s "$fastq_in" fastq_in.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 ln -s "$count_in" count_in.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 ln -s "$qfile_in" qfile_in.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 ln -s "$name_in" name_in.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 ln -s "$group_in" group_in.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 ln -s "$alignreport_in" alignreport_in.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 ln -s "$list_in" list_in.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 ln -s "$taxonomy_in" taxonomy_in.dat &&
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 echo 'get.seqs(
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 accnos=accnos.dat,
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 #if $fasta_in:
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 fasta=fasta_in.dat,
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 #end if
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 #if $fastq_in:
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 fastq=fastq_in.dat,
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 #end if
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 #if $count_in:
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 count=count_in.dat,
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 #end if
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 #if $qfile_in:
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 qfile=qfile_in.dat,
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 #end if
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 #if $name_in:
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 name=name_in.dat,
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 #end if
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 #if $group_in:
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 group=group_in.dat,
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 #end if
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 #if $alignreport_in:
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 alignreport=alignreport_in.dat,
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 #end if
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 #if $list_in:
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48 list=list_in.dat,
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49 #end if
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50 #if $taxonomy_in:
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51 taxonomy=taxonomy_in.dat,
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52 #end if
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53 dups=$dups
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54 )'
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55 | sed 's/ //g' ## mothur trips over whitespace
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 | mothur
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57 | tee mothur.out.log
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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58 ]]></command>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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59 <inputs>
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60 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/>
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61 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
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62 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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63 <param name="fastq_in" type="data" format="fastq" optional="true" label="count - a count_table" help="fastq - allows you to select sequences from your fastq file"/>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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64 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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65 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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66 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/>
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67 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
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68 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
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69 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
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70 <param name="dups" type="boolean" truevalue="dups" falsevalue="false" checked="true" label="dups - Apply to duplicates"/>
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71 </inputs>
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72 <outputs>
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73 <expand macro="logfile-output"/>
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74 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <filter>fasta_in</filter>
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76 </data>
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77 <data name="fastq_out" format_source="fastq_in" from_work_dir="fastq_in*.pick.*" label="${tool.name} on ${on_string}: pick.fastq">
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78 <filter>fastq_in</filter>
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79 </data>
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80 <data name="count_out" format_source="count_in" from_work_dir="count_in*.pick.*" label="${tool.name} on ${on_string}: pick.count">
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81 <filter>count_in</filter>
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82 </data>
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83 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.pick.*" label="${tool.name} on ${on_string}: pick.qfile">
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84 <filter>qfile_in</filter>
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85 </data>
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86 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
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87 <filter>name_in</filter>
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88 </data>
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89 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
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90 <filter>group_in</filter>
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91 </data>
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92 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.pick.*" label="${tool.name} on ${on_string}: pick.align.report">
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93 <filter>alignreport_in</filter>
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94 </data>
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95 <data name="list_out" format="mothur.list" from_work_dir="list_in*.pick.*" label="${tool.name} on ${on_string}: pick.list">
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96 <filter>list_in</filter>
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97 </data>
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98 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
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99 <filter>taxonomy_in</filter>
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100 </data>
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101 </outputs>
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102 <tests>
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103 <test>
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104 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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105 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
bfd467665e6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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106 <param name="dups" value=""/>
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107 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/>
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108 <expand macro="logfile-test"/>
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109 </test>
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110 <test>
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111 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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112 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
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113 <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/>
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114 <expand macro="logfile-test"/>
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115 </test>
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116 <test>
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117 <!-- test two input files -->
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118 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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119 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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120 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
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121 <param name="dups" value="false"/>
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122 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/>
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123 <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/>
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124 <expand macro="logfile-test"/>
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125 </test>
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126 <test>
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127 <param name="accnos" value="amazon.bad.accnos"/>
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128 <param name="count_in" value="amazon.count_table"/>
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129 <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/>
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130 <expand macro="logfile-test"/>
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131 </test>
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132 </tests>
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133 <help>
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134 <![CDATA[
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135
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136 @MOTHUR_OVERVIEW@
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137
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138 **Command Documentation**
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139
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140 The get.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection.
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141
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142 .. _name: https://www.mothur.org/wiki/Name_file
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143 .. _group: https://www.mothur.org/wiki/Group_file
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144 .. _list: https://www.mothur.org/wiki/List_file
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145 .. _align.report: https://www.mothur.org/wiki/Align.seqs
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146 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
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147 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
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148 .. _get.seqs: https://www.mothur.org/wiki/Get.seqs
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149
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150 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params
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151 ]]>
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152 </help>
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153 <expand macro="citations"/>
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154 </tool>