Mercurial > repos > iuc > mothur_get_relabund

annotate get.relabund.xml @ 0:05c1f352cf4e 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 16:34:15 -0400
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children 6495d62d9eb4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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05c1f352cf4e 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_relabund" name="Get.relabund" version="@WRAPPER_VERSION@.0">
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Calculate the relative abundance of each otu</description>
05c1f352cf4e 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>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
05c1f352cf4e 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
05c1f352cf4e 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 &&
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 echo 'get.relabund(
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 shared=otu.dat,
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #if $label:
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 label=${ str($label).replace(",","-") },
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #end if
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 #if $groups:
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 groups=${ str($groups).replace(",","-") },
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #end if
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 scale=$scale
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 )'
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 | sed 's/ //g' ## mothur trips over whitespace
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 | mothur
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 ]]></command>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 <inputs>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared" help="Use Make.shared to create a shared file from a list and a group file"/>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 <param name="label" type="select" label="label - OTU Labels" multiple="true">
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <expand macro="labeloptions"/>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 </param>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 <param name="groups" type="select" multiple="true" label="groups - Groups to consider">
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 <options>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <filter type="data_meta" ref="otu" key="groups"/>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 </options>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 </param>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <param name="scale" type="select" label="scale - Scale by">
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <option value="totalgroup" selected="true">Total Groups</option>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <option value="totalotu">Total OTUs</option>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <option value="averagegroup">Average Groups</option>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <option value="averageotu">Average OTUs</option>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 </param>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 </inputs>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <outputs>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <expand macro="logfile-output"/>
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44 <data name="relabund" format="mothur.relabund" from_work_dir="otu*.relabund" label="${tool.name} on ${on_string}: relabund"/>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <output name="relabund" file="amazon.an.relabund" ftype="mothur.relabund"/>
05c1f352cf4e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <expand macro="logfile-test"/>
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51 </test>
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52 <test>
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53 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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54 <param name="label" value="0.03,0.05,0.22"/>
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55 <param name="groups" value="forest"/>
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56 <output name="relabund" md5="3f91820ebdf2d4c640b7d1489fd67936" ftype="mothur.relabund"/>
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57 <expand macro="logfile-test"/>
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58 </test>
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59 </tests>
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60 <help>
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61 <![CDATA[
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62
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63 @MOTHUR_OVERVIEW@
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64
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65 **Command Documenation**
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66
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67 The get.relabund_ command calculates the relative abundance of each otu in a sample from a shared_ file. It outputs a .relabund_ file.
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68
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69 .. _shared: http://www.mothur.org/wiki/Shared_file
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70 .. _get.relabund: http://www.mothur.org/wiki/Get.relabund
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71
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72 v.1.21.0: Updated to Mothur 1.33
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73 ]]>
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74 </help>
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75 <expand macro="citations"/>
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76 </tool>