Mercurial > repos > iuc > mothur_list_otulabels

annotate list.otulabels.xml @ 3:9257cd34bb50 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author iuc
date Fri, 06 Apr 2018 04:21:15 -0400
parents 88e8819fb923
children e643cc6c39cb
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1 <tool profile="16.07" id="mothur_list_otulabels" name="List.otulabels" version="@WRAPPER_VERSION@.0">
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2 <description>Lists otu labels from shared or relabund 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
2
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15 echo 'list.otulabels(
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16 #if $otu.is_of_type("mothur.relabund"):
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17 relabund=otu.dat
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18 #elif $otu.is_of_type("mothur.shared"):
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19 shared=otu.dat
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20 #else
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21 list=otu.dat
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22 #end if
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23 #if $label:
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24 ,label=${ str($label).replace(",","-") }
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25 #end if
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26 #if $groups:
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27 ,groups=${ str($groups).replace(",","-") }
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28 #end if
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29 )'
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30 | sed 's/ //g' ## mothur trips over whitespace
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31 | mothur
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32 | tee mothur.out.log
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33 ]]></command>
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34 <inputs>
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35 <param name="otu" type="data" format="mothur.shared,mothur.relabund,mothur.list" label="list or shared or relabund - OTU List or Shared or Relabund"/>
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36 <param name="label" type="select" multiple="true" label="label - OTU Labels">
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37 <expand macro="labeloptions"/>
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38 </param>
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39 <param name="groups" type="select" multiple="true" label="groups - Pairwise comparision groups">
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40 <options>
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41 <filter type="data_meta" ref="otu" key="groups"/>
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42 </options>
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43 </param>
2
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44 <expand macro="param-savelog"/>
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45 </inputs>
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46 <outputs>
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47 <expand macro="logfile-output"/>
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48 <collection name="otulabels" type="list" label="${tool.name} on ${on_string}: otulabels">
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49 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otulabels" format="mothur.otulabels"/>
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50 </collection>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="infile" value="otulist"/>
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55 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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56 <output_collection name="otulabels" count="36">
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57 <element name="unique" md5="c901cebfbc87559f1667546111408a22" ftype="mothur.otulabels"/>
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58 <element name="0.55" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.otulabels"/>
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59 </output_collection>
2
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60 <param name="savelog" value="true"/>
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61 <expand macro="logfile-test"/>
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62 </test>
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63 <test><!-- test with group select -->
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64 <param name="infile" value="otulist"/>
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65 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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66 <param name="groups" value="forest"/>
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67 <output_collection name="otulabels" count="36">
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68 <element name="unique" md5="8a4d85496fdcfdf99337129989350e7e" ftype="mothur.otulabels"/>
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69 </output_collection>
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 </tests>
2
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74 <help><![CDATA[
0
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75
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76 @MOTHUR_OVERVIEW@
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77
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78 **Command Documentation**
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79
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80 The list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otus_ or remove.otulabels_ commands
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81
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82 .. _list.otulabels: https://www.mothur.org/wiki/List.otulabels
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83 .. _classify.otu: https://www.mothur.org/wiki/Classify.otu
e86c535cf4d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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84 .. _otu.association: https://www.mothur.org/wiki/Otu.association
e86c535cf4d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 .. _corr.axes: https://www.mothur.org/wiki/Corr.axes
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88e8819fb923 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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86 .. _get.otus: https://www.mothur.org/wiki/Get.otus
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e86c535cf4d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 .. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels
e86c535cf4d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 .. _shared: https://www.mothur.org/wiki/Shared_file
e86c535cf4d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 .. _relabund: https://www.mothur.org/wiki/Get.relabund
e86c535cf4d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90
e86c535cf4d1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 v.1.27.0: Updated to mothur 1.33, added list file for otu
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92
88e8819fb923 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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93 ]]></help>
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94 <expand macro="citations"/>
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95 </tool>