Mercurial > repos > iuc > mothur_normalize_shared

annotate normalize.shared.xml @ 0:ed349f5c32fe 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 16:42:45 -0400
parents
children 00df9f248874
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ed349f5c32fe 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_normalize_shared" name="Normalize.shared" version="@WRAPPER_VERSION@.0">
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Normalize the number of sequences per group to a specified level</description>
ed349f5c32fe 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>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
ed349f5c32fe 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"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
ed349f5c32fe 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 &&
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 echo 'normalize.shared(
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 #if $otu.is_of_type("mothur.relabund"):
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14 relabund=otu.dat
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 #elif $otu.is_of_type("mothur.shared"):
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 shared=otu.dat,
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 makerelabund=$makerelabund
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #end if
ed349f5c32fe 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(",","-") }
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #end if
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #if $groups:
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 ,groups=${ str($groups).replace(",","-") }
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #end if
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #if $method:
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 ,method=${ str($method).replace(",","-") }
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 #end if
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 )'
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 | sed 's/ //g' ## mothur trips over whitespace
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30 | mothur
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31 ]]></command>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <inputs>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
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34 <param name="label" type="select" multiple="true" label="label - OTU Labels">
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <expand macro="labeloptions"/>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 </param>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <options>
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39 <filter type="data_meta" ref="otu" key="groups"/>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 </options>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 </param>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <param name="method" type="select" label="method - Normalization method">
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43 <option value="totalgroup" selected="true">Total Group</option>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <option value="zscore">Z Score</option>
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45 </param>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <param name="makerelabund" type="boolean" truevalue="true" falsevalue="false" checked="false" label="makerelabund - convert a shared file to a relabund file before you normalize"/>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 </inputs>
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48 <outputs>
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49 <expand macro="logfile-output"/>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <collection name="sharedfiles" type="list" label="${tool.name} on ${on_string}: norm.shared files collection">
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.shared" format="mothur.shared"/>
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52 </collection>
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53 </outputs>
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54 <tests>
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55 <test><!-- test default settings -->
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56 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
ed349f5c32fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 <output_collection name="sharedfiles" count="36">
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58 <element name="0.26.norm" md5="73ad51ce74e5b3efbc1d9ec8ed6e1c07" ftype="mothur.shared"/>
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59 </output_collection>
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60 <expand macro="logfile-test"/>
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61 </test>
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62 <test><!-- test default settings -->
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63 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
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64 <param name="label" value="0.03,0.05,0.22,0.26"/>
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65 <param name="groups" value="forest,pasture"/>
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66 <param name="method" value="zscore"/>
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67 <output_collection name="sharedfiles" count="4">
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68 <element name="0.26.norm" md5="1204d65c732fd880585180e956610026" ftype="mothur.shared"/>
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69 </output_collection>
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70 <expand macro="logfile-test"/>
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71 </test>
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72 </tests>
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73 <help>
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74 <![CDATA[
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75
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76 @MOTHUR_OVERVIEW@
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77
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78 **Command Documenation**
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79
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80 The normalize.shared_ command normalizes the number of sequences per group to a specified level. The input is a shared_ or relabund_ file.
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81
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82 .. _shared: http://www.mothur.org/wiki/Shared_file
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83 .. _relabund: http://www.mothur.org/wiki/Get.relabund
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84 .. _normalize.shared: http://www.mothur.org/wiki/Normalize.shared
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85 ]]>
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86 </help>
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87 <expand macro="citations"/>
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88 </tool>