Mercurial > repos > iuc > mothur_get_relabund

annotate get.relabund.xml @ 3:c992d9efe919 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author iuc
date Fri, 06 Apr 2018 04:05:22 -0400
parents 47e9c119ac28
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1 <tool profile="16.07" id="mothur_get_relabund" name="Get.relabund" version="@WRAPPER_VERSION@.0">
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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>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$otu' otu.dat &&
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14
2
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15 echo 'get.relabund(
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16 shared=otu.dat,
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17 #if $label:
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18 label=${ str($label).replace(",","-") },
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19 #end if
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20 #if $groups:
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21 groups=${ str($groups).replace(",","-") },
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22 #end if
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23 scale=$scale
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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
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28 ]]></command>
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29 <inputs>
2
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30 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"
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31 help="Use Make.shared to create a shared file from a list and a group file"/>
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32 <param name="label" type="select" label="label - OTU Labels" multiple="true">
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33 <expand macro="labeloptions"/>
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34 </param>
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35 <param name="groups" type="select" multiple="true" label="groups - Groups to consider">
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36 <options>
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37 <filter type="data_meta" ref="otu" key="groups"/>
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38 </options>
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39 </param>
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40 <param name="scale" type="select" label="scale - Scale by">
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41 <option value="totalgroup" selected="true">Total Groups</option>
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42 <option value="totalotu">Total OTUs</option>
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43 <option value="averagegroup">Average Groups</option>
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44 <option value="averageotu">Average OTUs</option>
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45 </param>
2
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46 <expand macro="param-savelog"/>
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47 </inputs>
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48 <outputs>
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49 <expand macro="logfile-output"/>
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50 <data name="relabund" format="mothur.relabund" from_work_dir="otu*.relabund" label="${tool.name} on ${on_string}: relabund"/>
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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55 <output name="relabund" file="amazon.an.relabund" ftype="mothur.relabund"/>
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56 <param name="savelog" value="true"/>
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57 <expand macro="logfile-test"/>
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58 </test>
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59 <test>
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60 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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61 <param name="label" value="0.03,0.05,0.22"/>
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62 <param name="groups" value="forest"/>
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63 <output name="relabund" md5="3f91820ebdf2d4c640b7d1489fd67936" ftype="mothur.relabund"/>
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64 <param name="savelog" value="true"/>
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65 <expand macro="logfile-test"/>
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66 </test>
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67 </tests>
2
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68 <help><![CDATA[
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69
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70 @MOTHUR_OVERVIEW@
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71
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72 **Command Documentation**
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73
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74 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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75
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76 .. _shared: https://www.mothur.org/wiki/Shared_file
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77 .. _get.relabund: https://www.mothur.org/wiki/Get.relabund
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78
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79 v.1.21.0: Updated to Mothur 1.33
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80
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81 ]]></help>
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82 <expand macro="citations"/>
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83 </tool>