Mercurial > repos > iuc > mothur_create_database

annotate create.database.xml @ 6:319884cd49a3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author iuc
date Mon, 02 Dec 2019 06:32:00 -0500
parents 024a52bdf70c
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1 <tool profile="16.07" id="mothur_create_database" name="Create.database" version="@WRAPPER_VERSION@.0">
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2 <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$otu' otu.dat &&
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14 ln -s '$repfasta' repfasta.dat &&
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15 ln -s '$nameOrCount' nameOrCount.dat &&
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16 ln -s '$constaxonomy' constaxonomy.dat &&
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17 ln -s '$group' group.dat &&
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18
2
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19 echo 'create.database(
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20 #if $otu.is_of_type("mothur.list"):
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21 list=otu.dat
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22 #elif $otu.is_of_type("mothur.shared"):
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23 shared=otu.dat
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24 #end if
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25 ,repfasta=repfasta.dat
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26 #if $nameOrCount.is_of_type("mothur.names"):
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27 ,repname=nameOrCount.dat
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28 #elif $nameOrCount.is_of_type("mothur.count_table"):
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29 ,count=nameOrCount.dat
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30 #end if
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31 ,constaxonomy=constaxonomy.dat
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32 #if $group:
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33 ,group=group.dat
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34 #end if
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35 #if $label:
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36 ,label=$label
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37 #end if
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38 )'
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39 | sed 's/ //g' ## mothur trips over whitespace
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40 | mothur
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41 | tee mothur.out.log
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42 ]]></command>
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43 <inputs>
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44 <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/>
2
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45 <param name="repfasta" type="data" format="fasta" optional="true" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/>
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46 <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" label="repname/count - Representative sequences"
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47 help="rep.name file or rep.count_table file generated by get.oturep"/>
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48 <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy"
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49 help="consensus taxonomy file output by classify.otu"/>
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50 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
2
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51 <param name="label" type="select" label="label - OTU Labels" optional="true"
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52 help="Select exactly one label. If none selected, first label in your list or shared file will be used">
0
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53 <expand macro="labeloptions"/>
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54 </param>
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55 <expand macro="param-savelog"/>
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56 </inputs>
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57 <outputs>
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58 <expand macro="logfile-output"/>
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59 <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/>
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60 </outputs>
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61 <tests>
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62 <!-- Test with a mothur.names file -->
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63 <test>
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64 <param name="otu" value="cd-test.list" ftype="mothur.list"/>
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65 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
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66 <param name="nameOrCount" value="cd-test.repname" ftype="mothur.names"/>
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67 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
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68 <param name="label" value="unique"/>
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69 <output name="database" file="cd-test.database" ftype="tabular"/>
2
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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 with a mothur.count_table file -->
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74 <test>
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75 <param name="otu" value="cd-test.list" ftype="mothur.list"/>
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76 <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
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77 <param name="nameOrCount" value="cd-test.count_table" ftype="mothur.count_table"/>
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78 <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
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79 <param name="label" value="unique"/>
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80 <output name="database" file="cd-test.database" ftype="tabular"/>
2
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81 <param name="savelog" value="true"/>
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82 <expand macro="logfile-test"/>
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83 </test>
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84 </tests>
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85 <help><![CDATA[
0
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86
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87 @MOTHUR_OVERVIEW@
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88
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89 **Command Documentation**
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90
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91 The create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file.
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92
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93 .. _list: https://www.mothur.org/wiki/List_file
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94 .. _shared: https://www.mothur.org/wiki/Shared_file
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95 .. _create.database: https://www.mothur.org/wiki/Create.database
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96
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97 v.1.28.0: Updated to Mothur 1.33, added count paramter.
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98
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99 ]]></help>
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100 <expand macro="citations"/>
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101 </tool>