Mercurial > repos > iuc > mothur_get_otus

annotate get.otus.xml @ 1:054caee6f6e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:13:20 -0400
parents 43d0b4bf9f1a
children 73f7faafd5ee
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>
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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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054caee6f6e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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7 <expand macro="stdio"/>
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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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8 <expand macro="version_command"/>
1
054caee6f6e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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9 <command><![CDATA[
054caee6f6e8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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10 @SHELL_OPTIONS@
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11
0
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12 ## 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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13 ln -s "$otu" otu.dat &&
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$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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15 #if $groupnames.source == 'accnos':
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 ln -s "$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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17 #end if
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18
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19 echo 'get.otus(
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 list=otu.dat,
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 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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22 #if $label:
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 ,label=${ str($label).replace(",","-") }
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #end if
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #if $groupnames.source == 'groups':
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 ,groups=${ 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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27 #else
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 ,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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29 #end if
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30 )'
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31 | 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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32 | mothur
1
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33 | tee mothur.out.log
0
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34 ]]></command>
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35 <inputs>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <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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37 <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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38 <expand macro="labeloptions"/>
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39 </param>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <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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41 <conditional name="groupnames">
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42 <param name="source" type="select" label="Select Group Names from">
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43 <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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44 <option value="accnos">A History Group Name Accnos Dataset</option>
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45 </param>
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46 <when value="groups">
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <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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48 <help>At least one group must be selected</help>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <options>
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50 <filter type="data_meta" ref="group_in" key="groups"/>
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51 </options>
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52 </param>
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53 </when>
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54 <when value="accnos">
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55 <param name="accnos_in" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 </when>
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57 </conditional>
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58 </inputs>
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59 <outputs>
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60 <expand macro="logfile-output"/>
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61 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
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63 </outputs>
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64 <tests>
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65 <test><!-- test with group file -->
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66 <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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67 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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68 <param name="source" value="groups"/>
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69 <param name="groups" value="forest,pasture"/>
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70 <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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71 <output name="group_out" md5="954ef97da9dcd152b912bcda19a6f96c" ftype="mothur.groups"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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72 <expand macro="logfile-test"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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73 </test>
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74 <test><!-- test with accnos file and label select -->
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75 <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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76 <param name="label" value="0.03"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <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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78 <param name="source" value="accnos"/>
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79 <param name="accnos_in" value="amazon.groupaccnos" ftype="mothur.accnos"/>
43d0b4bf9f1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <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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81 <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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82 <expand macro="logfile-test"/>
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83 </test>
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84 </tests>
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85 <help>
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86 <![CDATA[
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87
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88 @MOTHUR_OVERVIEW@
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89
1
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90 **Command Documentation**
0
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91
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92 The get.otus_ command selects otus from a list_ containing sequences from a specific group or set of groups.
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93
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94 .. _list: https://www.mothur.org/wiki/List_file
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95 .. _get.otus: https://www.mothur.org/wiki/Get.otus
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96
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97 v.1.20.0: Updated to Mothur 1.33
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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>