Mercurial > repos > iuc > mothur_get_rabund

annotate get.rabund.xml @ 3:4b702fcdcd36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:41:38 -0500
parents bd8b854bdb00
children b5025af79eac
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1 <tool profile="16.07" id="mothur_get_rabund" name="Get.rabund" version="@WRAPPER_VERSION@.0">
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2 <description>Get rabund from a otu list or sabund</description>
31b9f13b80a6 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>
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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[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$count' count.dat &&
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$otu' otu.dat &&
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31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15
3
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16 echo 'get.rabund(
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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17 #if $label:
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18 label=${ str($label).replace(",","-") },
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 #end if
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 #if $count:
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 count=count.dat,
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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22 #end if
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 #if $otu.is_of_type("mothur.list"):
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 list=otu.dat,
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 #elif $otu.is_of_type("mothur.sabund"):
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 sabund=otu.dat,
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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27 #end if
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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28 sorted=$sorted
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 )'
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30 | sed 's/ //g' ## mothur trips over whitespace
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 | mothur
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 | tee mothur.out.log
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31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 ]]></command>
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34 <inputs>
31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <param name="otu" type="data" format="mothur.list,mothur.sabund" label="list,sabund - List or Sabund"/>
31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <expand macro="labeloptions"/>
31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 </param>
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39 <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - sort by abundance"
4b702fcdcd36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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40 help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/>
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31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 </inputs>
31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <outputs>
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44 <expand macro="logfile-output"/>
31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <data name="rabund" format="mothur.rabund" from_work_dir="otu*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
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46 </outputs>
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47 <tests>
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48 <test><!-- test sabund input -->
31b9f13b80a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
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50 <param name="label" value="0.03,0.05"/>
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51 <output name="rabund" file="amazon.an.rabund2" ftype="mothur.rabund"/>
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52 <expand macro="logfile-test"/>
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53 </test>
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54 <test><!-- test otu list input -->
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55 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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56 <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/>
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57 <expand macro="logfile-test"/>
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58 </test>
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59 </tests>
3
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60 <help><![CDATA[
0
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61
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62 @MOTHUR_OVERVIEW@
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63
1
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64 **Command Documentation**
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65
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66 The get.rabund_ command generates an rabund_ file from a list_ or sabund_ file.
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67
1
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68 .. _rabund: https://www.mothur.org/wiki/Rabund_file
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69 .. _list: https://www.mothur.org/wiki/List_file
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70 .. _sabund: https://www.mothur.org/wiki/Sabund_file
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71 .. _get.rabund: https://www.mothur.org/wiki/Get.rabund
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72
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73 ]]></help>
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74 <expand macro="citations"/>
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75 </tool>