Mercurial > repos > iuc > mothur_make_shared

annotate make.shared.xml @ 0:b8947620846f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:08:32 -0400
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children c4b6d7acffbf
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b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_make_shared" name="Make.shared" version="@WRAPPER_VERSION@.0">
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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2 <description>Make a shared file from a list and a group</description>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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4 <import>macros.xml</import>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$intype.otu" intype_otu.dat &&
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 #if $intype.infile == "otulist":
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ln -s "$intype.group" intype_group.dat &&
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 #end if
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17
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 echo 'make.shared(
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 #if $intype.infile == "biom":
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 biom=intype_otu.dat
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 #else
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22 #if $intype.group.is_of_type("mothur.groups"):
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 group=intype_group.dat,
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 #elif $intype.group.is_of_type("mothur.count_table"):
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 count=intype_group.dat,
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 #end if
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 #if $intype.label:
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 label=${ str($intype.label).replace(",","-") },
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 #end if
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 #if $intype.groups:
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 groups=${ str($intype.groups).replace(",","-") },
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 #end if
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 list=intype_otu.dat
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 #end if
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 )'
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 | sed 's/ //g' ## mothur trips over whitespace
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 | mothur
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 | tee mothur.out.log &&
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 ## move output files to correct destination
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 mv mothur.*.logfile "$logfile" &&
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 #if $intype.infile == 'otulist' and $intype.groups:
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43 mv intype_otu*.groups "$groupout"
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 #else
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45 mv intype_otu*.shared "$shared"
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 #end if
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47 ]]></command>
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48 <inputs>
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49 <conditional name="intype">
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50 <param name="infile" type="select" label="Select input type" help="">
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51 <option value="otulist">OTU list</option>
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52 <option value="biom">Biom 1.0 file</option>
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53 </param>
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54 <when value="otulist">
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55 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 <param name="group" type="data" format="mothur.groups, mothur.count_table" label="supply group or count table if you supplied OTU list"/>
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57 <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.">
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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58 <expand macro="labeloptions"/>
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59 </param>
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60 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
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61 <options>
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62 <filter type="data_meta" ref="group" key="groups"/>
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63 </options>
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64 </param>
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65 </when>
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66 <when value="biom">
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67 <param name="otu" type="data" format="biom1" label="Biom 1.0 file"/>
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68 </when>
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69 </conditional>
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70 </inputs>
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71 <outputs>
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72 <expand macro="logfile-output"/>
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73 <data name="shared" format="mothur.shared" from_work_dir="intype_otu*.shared" label="${tool.name} on ${on_string}: shared"/>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 <data name="groupout" format="mothur.groups" from_work_dir="intype_otu*.groups" label="${tool.name} on ${on_string}: groups">
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <filter>intype['group'].ext == "mothur.groups"</filter>
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76 </data>
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77 <collection name="labelshares" type="list" label="${tool.name} on ${on_string}: share files per label">
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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79 <filter>intype['groups']</filter>
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80 </collection>
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81 </outputs>
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82 <tests>
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83 <test><!-- test with biom file -->
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84 <param name="infile" value="biom"/>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 <param name="otu" value="example.biom"/>
b8947620846f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 <output name="shared" md5="e44d5ca4e4a5dbc68e8219c5690aa156" ftype="mothur.shared"/>
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87 <expand macro="logfile-test"/>
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88 </test>
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89 <test><!-- test with otu and group file-->
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90 <param name="infile" value="otulist"/>
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91 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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92 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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93 <output name="shared" file="amazon.an.shared" ftype="mothur.shared"/>
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94 <expand macro="logfile-test"/>
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95 </test>
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96 <test><!-- test with label and group select-->
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97 <param name="infile" value="otulist"/>
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98 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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99 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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100 <param name="label" value="0.03,0.05,0.22"/>
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101 <param name="groups" value="forest,pasture"/>
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102 <output name="groupout" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/>
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103 <output_collection name="labelshares" count="3">
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104 <element name="0.22" md5="592b4fb84412de47be18e64ef26b7a80" ftype="mothur.shared"/>
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105 </output_collection>
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106 <expand macro="logfile-test"/>
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107 </test>
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108 </tests>
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109 <help>
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110 <![CDATA[
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111
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112 @MOTHUR_OVERVIEW@
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113
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114 **Command Documentation**
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115
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116 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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117
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118
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119 .. _list: https://www.mothur.org/wiki/List_file
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120 .. _group: https://www.mothur.org/wiki/Group_file
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121 .. _shared: https://www.mothur.org/wiki/Shared_file
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122 .. _rabund: https://www.mothur.org/wiki/Rabund_file
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123 .. _make.shared: https://www.mothur.org/wiki/Make.shared
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124 ]]>
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125 </help>
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126 <expand macro="citations"/>
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127 </tool>