Mercurial > repos > iuc > mothur_deunique_seqs

annotate deunique.seqs.xml @ 0:57cf9fc6c84a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:29:24 -0400
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children 623e22d7cb82
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_deunique_seqs" name="Deunique.seqs" version="@WRAPPER_VERSION@.0">
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Return all sequences</description>
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3 <macros>
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iuc
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$fasta" fasta.dat &&
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$names" names.dat &&
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 echo 'deunique.seqs(
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #if $inputtype.intype == "countfile":
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 count=names.dat,
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #else
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17 name=names.dat,
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #end if
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19 fasta=fasta.dat
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 )'
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 | sed 's/ //g' ## mothur trips over whitespace
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 | mothur
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 ]]></command>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 <inputs>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 <conditional name="inputtype">
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help="">
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <option value="namesfile">names</option>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 <option value="countfile">count table</option>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 </param>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 <when value="namesfile">
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <param name="names" type="data" format="mothur.names" label="provide a names file" help="A names file will generate a new faste file containing all the sequences."/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 </when>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <when value="countfile">
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <param name="names" type="data" format="mothur.count_table" label="provide a count table" help="A counts table will generate a new faste file containing all the sequences. If the file contains group information, a group file will also be created."/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 </when>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 </conditional>
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38 </inputs>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <outputs>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <expand macro="logfile-output"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.redundant.fasta" label="${tool.name} on ${on_string}: fasta"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <!-- groups file is created when a count file is used as input, but will be empty if the count file did not contain group information -->
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <data name="groups_file" format="mothur.groups" from_work_dir="names.redundant.groups" label="${tool.name} on ${on_string}: groups">
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <filter>inputtype.intype == 'countfile'</filter>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 </data>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 </outputs>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <tests>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <test><!-- test names file input -->
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <param name="fasta" value="amazon.unique.fasta"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <param name="intype" value="namesfile"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 <param name="names" value="amazon.unique.names"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 <expand macro="logfile-test"/>
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54 </test>
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55 <test><!-- test count file input with group file output -->
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <param name="fasta" value="amazon.unique.fasta"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 <param name="intype" value="countfile"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <param name="names" value="amazon_withgroups.count_table"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 <expand macro="logfile-test"/>
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62 </test>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <test><!-- test count file input without group file output -->
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 <param name="fasta" value="amazon.unique.fasta"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <param name="intype" value="countfile"/>
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66 <param name="names" value="amazon.count_table"/>
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67 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty-->
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 <expand macro="logfile-test"/>
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70 </test>
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71 </tests>
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72 <help>
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73 <![CDATA[
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74
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75 @MOTHUR_OVERVIEW@
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76
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77 **Command Documenation**
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78
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79 The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80
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81 .. _name: http://www.mothur.org/wiki/Name_file
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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82 .. _deunique.seqs: http://www.mothur.org/wiki/Deunique.seqs
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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83
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84 v.1.21.0: Updated to Mothur 1.33, added option to provide count instead of names file, new groups file as output
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85
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86 ]]>
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87 </help>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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parents:
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88 <expand macro="citations"/>
57cf9fc6c84a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
89 </tool>