Mercurial > repos > iuc > mothur_deunique_seqs

annotate deunique.seqs.xml @ 10:3767f899f13c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 13:11:24 +0000
parents 3291237294fe
children
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4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_deunique_seqs" name="Deunique.seqs" version="@WRAPPER_VERSION@.0">
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Return all sequences</description>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
10
3767f899f13c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
2
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11 @SHELL_OPTIONS@
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12
2
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13 ## create symlinks to input datasets
3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$fasta' fasta.dat &&
3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$names' names.dat &&
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16
2
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17 echo 'deunique.seqs(
3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 #if $inputtype.intype == "countfile":
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19 count=names.dat,
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20 #else
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21 name=names.dat,
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22 #end if
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23 fasta=fasta.dat
3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 )'
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25 | sed 's/ //g' ## mothur trips over whitespace
3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 | mothur
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27 | tee mothur.out.log
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28 ]]></command>
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29 <inputs>
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30 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to filter"/>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 <conditional name="inputtype">
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 <param name="intype" type="select" label="type of file to provide, may be either a names or a count file" help="">
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <option value="namesfile">names</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 <option value="countfile">count table</option>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 </param>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 <when value="namesfile">
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <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."/>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 </when>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <when value="countfile">
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40 <param name="names" type="data" format="mothur.count_table" label="provide a count table"
3291237294fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 help="A counts table will generate a new faste file containing all the sequences.
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42 If the file contains group information, a group file will also be created."/>
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43 </when>
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44 </conditional>
2
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45 <expand macro="param-savelog"/>
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46 </inputs>
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47 <outputs>
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48 <expand macro="logfile-output"/>
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49 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.redundant.fasta" label="${tool.name} on ${on_string}: fasta"/>
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50 <!-- groups file is created when a count file is used as input, but will be empty if the count file did not contain group information -->
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51 <data name="groups_file" format="mothur.groups" from_work_dir="names.redundant.groups" label="${tool.name} on ${on_string}: groups">
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52 <filter>inputtype.intype == 'countfile'</filter>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test><!-- test names file input -->
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57 <param name="fasta" value="amazon.unique.fasta"/>
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58 <param name="intype" value="namesfile"/>
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59 <param name="names" value="amazon.unique.names"/>
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60 <output name="out_fasta" md5="579698b8037ee939dd730e2cf0dd018d" ftype="fasta"/>
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61 <param name="savelog" value="true"/>
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62 <expand macro="logfile-test"/>
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63 </test>
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64 <test><!-- test count file input with group file output -->
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65 <param name="fasta" value="amazon.unique.fasta"/>
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66 <param name="intype" value="countfile"/>
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67 <param name="names" value="amazon_withgroups.count_table"/>
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68 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
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69 <output name="groups_file" file="amazon_withgroups.redundant.groups" ftype="mothur.groups"/>
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70 <param name="savelog" value="true"/>
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71 <expand macro="logfile-test"/>
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72 </test>
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73 <test><!-- test count file input without group file output -->
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74 <param name="fasta" value="amazon.unique.fasta"/>
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <param name="intype" value="countfile"/>
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76 <param name="names" value="amazon.count_table"/>
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77 <output name="out_fasta" md5="177f5cf92a84ab3aef0a665e06178bbe" ftype="fasta"/>
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78 <output name="groups_file" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.groups"/> <!--empty-->
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79 <param name="savelog" value="true"/>
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80 <expand macro="logfile-test"/>
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81 </test>
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82 </tests>
2
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83 <help><![CDATA[
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84
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85 @MOTHUR_OVERVIEW@
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86
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87 **Command Documentation**
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88
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89 The deunique.seqs_ command is the reverse of the unique.seqs command, and creates a fasta file from a fasta and name_ file.
4b2dabf45996 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90
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91 .. _name: https://www.mothur.org/wiki/Name_file
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92 .. _deunique.seqs: https://www.mothur.org/wiki/Deunique.seqs
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93
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94 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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95
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96 ]]></help>
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97 <expand macro="citations"/>
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98 </tool>