Mercurial > repos > iuc > mothur_make_shared

annotate make.shared.xml @ 0:e9d1265e868e 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 16:38:49 -0400
parents
children 5f23107faaa8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_make_shared" name="Make.shared" version="@WRAPPER_VERSION@.0" force_history_refresh="True">
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Make a shared file from a list and a group</description>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8 <command detect_errors="aggressive"><![CDATA[
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$intype.otu" intype_otu.dat &&
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 #if $intype.infile == "otulist":
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$intype.group" intype_group.dat &&
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 #end if
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 echo 'make.shared(
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #if $intype.infile == "biom":
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 biom=intype_otu.dat
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #else
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #if $intype.group.is_of_type("mothur.groups"):
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 group=intype_group.dat,
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #elif $intype.group.is_of_type("mothur.count_table"):
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 count=intype_group.dat,
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #end if
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #if $intype.label:
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 label=${ str($intype.label).replace(",","-") },
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #end if
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 #if $intype.groups:
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 groups=${ str($intype.groups).replace(",","-") },
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #end if
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 list=intype_otu.dat
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 #end if
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 )'
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 | sed 's/ //g' ## mothur trips over whitespace
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 | mothur &&
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 ## move output files to correct destination
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 mv mothur.*.logfile "$logfile" &&
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 #if $intype.infile == 'otulist' and $intype.groups:
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 mv intype_otu*.groups "$groupout"
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 #else
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 mv intype_otu*.shared "$shared"
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 #end if
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 ]]></command>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <inputs>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <conditional name="intype">
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46 <param name="infile" type="select" label="Select input type" help="">
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <option value="otulist">OTU list</option>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <option value="biom">Biom 1.0 file</option>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 </param>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <when value="otulist">
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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52 <param name="group" type="data" format="mothur.groups, mothur.count_table" label="supply group or count table if you supplied OTU list"/>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
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54 <expand macro="labeloptions"/>
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55 </param>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
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57 <options>
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58 <filter type="data_meta" ref="group" key="groups"/>
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59 </options>
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60 </param>
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61 </when>
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62 <when value="biom">
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63 <param name="otu" type="data" format="biom1" label="Biom 1.0 file"/>
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64 </when>
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65 </conditional>
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66 </inputs>
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67 <outputs>
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68 <expand macro="logfile-output"/>
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69 <data name="shared" format="mothur.shared" from_work_dir="intype_otu*.shared" label="${tool.name} on ${on_string}: shared"/>
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70 <data name="groupout" format="mothur.groups" from_work_dir="intype_otu*.groups" label="${tool.name} on ${on_string}: groups">
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71 <filter>groups</filter>
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72 </data>
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73 <collection name="labelshares" type="list" label="${tool.name} on ${on_string}: share files per label">
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74 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <filter>groups</filter>
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76 </collection>
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77 </outputs>
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78 <tests>
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79 <test><!-- test with biom file -->
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80 <param name="infile" value="biom"/>
e9d1265e868e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <param name="otu" value="example.biom"/>
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82 <output name="shared" md5="e44d5ca4e4a5dbc68e8219c5690aa156" ftype="mothur.shared"/>
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83 <expand macro="logfile-test"/>
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84 </test>
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85 <test><!-- test with otu and group file-->
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86 <param name="infile" value="otulist"/>
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87 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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88 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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89 <output name="shared" file="amazon.an.shared" ftype="mothur.shared"/>
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90 <expand macro="logfile-test"/>
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91 </test>
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92 <test><!-- test with label and group select-->
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93 <param name="infile" value="otulist"/>
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94 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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95 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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96 <param name="label" value="0.03,0.05,0.22"/>
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97 <param name="groups" value="forest,pasture"/>
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98 <output name="groupout" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
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99 <output_collection name="labelshares" count="3">
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100 <element name="0.22" md5="592b4fb84412de47be18e64ef26b7a80" ftype="mothur.shared"/>
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101 </output_collection>
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102 <expand macro="logfile-test"/>
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103 </test>
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104 </tests>
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105 <help>
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106 <![CDATA[
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107
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108 @MOTHUR_OVERVIEW@
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109
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110 **Command Documenation**
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111
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112 The make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group.
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113
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114
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115 .. _list: http://www.mothur.org/wiki/List_file
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116 .. _group: http://www.mothur.org/wiki/Group_file
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117 .. _shared: http://www.mothur.org/wiki/Shared_file
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118 .. _rabund: http://www.mothur.org/wiki/Rabund_file
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119 .. _make.shared: http://www.mothur.org/wiki/Make.shared
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120 ]]>
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121 </help>
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122 <expand macro="citations"/>
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123 </tool>