Mercurial > repos > iuc > mothur_get_relabund

annotate get.relabund.xml @ 0:4ad3ea2f8584 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 05:46:09 -0400
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children 47e9c119ac28
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0
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_get_relabund" name="Get.relabund" version="@WRAPPER_VERSION@.0">
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Calculate the relative abundance of each otu</description>
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3 <macros>
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4 <import>macros.xml</import>
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
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6 <expand macro="requirements"/>
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
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13 ln -s "$otu" otu.dat &&
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14
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15 echo 'get.relabund(
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 shared=otu.dat,
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 #if $label:
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18 label=${ str($label).replace(",","-") },
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 #end if
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 #if $groups:
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 groups=${ str($groups).replace(",","-") },
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 #end if
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23 scale=$scale
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 )'
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25 | sed 's/ //g' ## mothur trips over whitespace
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26 | mothur
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27 | tee mothur.out.log
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 ]]></command>
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 <inputs>
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30 <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"/>
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 <param name="label" type="select" label="label - OTU Labels" multiple="true">
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 <expand macro="labeloptions"/>
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33 </param>
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34 <param name="groups" type="select" multiple="true" label="groups - Groups to consider">
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35 <options>
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36 <filter type="data_meta" ref="otu" key="groups"/>
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 </options>
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38 </param>
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39 <param name="scale" type="select" label="scale - Scale by">
4ad3ea2f8584 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <option value="totalgroup" selected="true">Total Groups</option>
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41 <option value="totalotu">Total OTUs</option>
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42 <option value="averagegroup">Average Groups</option>
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43 <option value="averageotu">Average OTUs</option>
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44 </param>
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45 </inputs>
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46 <outputs>
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47 <expand macro="logfile-output"/>
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48 <data name="relabund" format="mothur.relabund" from_work_dir="otu*.relabund" label="${tool.name} on ${on_string}: relabund"/>
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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53 <output name="relabund" file="amazon.an.relabund" ftype="mothur.relabund"/>
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54 <expand macro="logfile-test"/>
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55 </test>
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56 <test>
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57 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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58 <param name="label" value="0.03,0.05,0.22"/>
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59 <param name="groups" value="forest"/>
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60 <output name="relabund" md5="3f91820ebdf2d4c640b7d1489fd67936" ftype="mothur.relabund"/>
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61 <expand macro="logfile-test"/>
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62 </test>
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63 </tests>
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64 <help>
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65 <![CDATA[
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66
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67 @MOTHUR_OVERVIEW@
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68
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69 **Command Documentation**
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70
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71 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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72
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73 .. _shared: https://www.mothur.org/wiki/Shared_file
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74 .. _get.relabund: https://www.mothur.org/wiki/Get.relabund
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75
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76 v.1.21.0: Updated to Mothur 1.33
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77 ]]>
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78 </help>
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79 <expand macro="citations"/>
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80 </tool>