Mercurial > repos > iuc > mothur_get_otus

annotate get.otus.xml @ 0:43d0b4bf9f1a 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 16:33:43 -0400
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children 054caee6f6e8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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43d0b4bf9f1a 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_get_otus" name="Get.otus" version="@WRAPPER_VERSION@.0">
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Get otus containing sequences from specified groups</description>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$otu" otu.dat &&
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$group_in" group_in.dat &&
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 #if $groupnames.source == 'accnos':
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$groupnames.accnos_in" groupnames.accnos_in.dat &&
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #end if
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15
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 echo 'get.otus(
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 list=otu.dat,
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 group=group_in.dat
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #if $label:
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20 ,label=${ str($label).replace(",","-") }
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #end if
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22 #if $groupnames.source == 'groups':
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 ,groups=${ str($groupnames.groups).replace(",","-") }
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #else
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 ,accnos=groupnames.accnos_in.dat
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #end if
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27 )'
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28 | sed 's/ //g' ## mothur trips over whitespace
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 | mothur
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30 ]]></command>
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31 <inputs>
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32 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <param name="label" type="select" optional="true" multiple="false" label="label - OTU Label" help="select exactly one label. If none selected, the first label in your file will be used">
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <expand macro="labeloptions"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 </param>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <conditional name="groupnames">
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38 <param name="source" type="select" label="Select Group Names from">
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <option value="groups">A List of Group Names</option>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <option value="accnos">A History Group Name Accnos Dataset</option>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 </param>
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42 <when value="groups">
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <param name="groups" type="select" multiple="true" force_select="true" label="groups - Pick groups to include">
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <help>At least one group must be selected</help>
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45 <options>
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46 <filter type="data_meta" ref="group_in" key="groups"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 </options>
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48 </param>
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49 </when>
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50 <when value="accnos">
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51 <param name="accnos_in" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
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52 </when>
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53 </conditional>
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54 </inputs>
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55 <outputs>
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56 <expand macro="logfile-output"/>
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57 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/>
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58 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
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59 </outputs>
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60 <tests>
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61 <test><!-- test with group file -->
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62 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 <param name="source" value="groups"/>
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65 <param name="groups" value="forest,pasture"/>
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66 <output name="list_out" md5="a771e0879bbb84e2764db70f66ae1277" ftype="mothur.list"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 <output name="group_out" md5="954ef97da9dcd152b912bcda19a6f96c" ftype="mothur.groups"/>
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68 <expand macro="logfile-test"/>
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69 </test>
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70 <test><!-- test with accnos file and label select -->
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71 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 <param name="label" value="0.03"/>
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73 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <param name="source" value="accnos"/>
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75 <param name="accnos_in" value="amazon.groupaccnos" ftype="mothur.accnos"/>
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76 <output name="list_out" md5="2069739b1f7bbbe47cc237833450e57c" ftype="mothur.list"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <output name="group_out" md5="09ffabe975dc49f1bf251ea60c569526" ftype="mothur.groups"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 <expand macro="logfile-test"/>
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79 </test>
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80 </tests>
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81 <help>
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82 <![CDATA[
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83
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84 @MOTHUR_OVERVIEW@
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85
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86 **Command Documenation**
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87
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88 The get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups.
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89
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90 .. _list: http://www.mothur.org/wiki/List_file
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91 .. _get.otus: http://www.mothur.org/wiki/Get.otus
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92
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93 v.1.20.0: Updated to Mothur 1.33
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94 ]]>
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95 </help>
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96 <expand macro="citations"/>
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97 </tool>