Mercurial > repos > iuc > mothur_get_sabund

annotate get.sabund.xml @ 0:579ffc8e2b4b 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 05:36:09 -0400
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children 502c0ba699fb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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579ffc8e2b4b 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_sabund" name="Get.sabund" version="@WRAPPER_VERSION@.0">
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Get sabund from a otu list or rabund</description>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$otu" otu.dat &&
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$count" count.dat &&
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15
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16 echo 'get.sabund(
579ffc8e2b4b 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(",","-") },
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 #end if
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 #if $count:
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 count=count.dat,
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 #end if
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 #if $otu.is_of_type("mothur.list"):
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 list=otu.dat
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 #elif $otu.is_of_type("mothur.rabund"):
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 rabund=otu.dat
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 #end if
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 )'
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 | sed 's/ //g' ## mothur trips over whitespace
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 | mothur
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 | tee mothur.out.log
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 ]]></command>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <inputs>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 <param name="otu" type="data" format="mothur.list,mothur.rabund" label="list,rabund - List or Rabund"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 <param name="label" type="select" optional="true" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 <expand macro="labeloptions"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 </param>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <param name="count" type="data" format="mothur.count_table" optional="true" help="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 </inputs>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <outputs>
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41 <expand macro="logfile-output"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 <data name="sabund" format="mothur.sabund" from_work_dir="otu*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 </outputs>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 <tests>
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45 <test><!-- test rabund input -->
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46 <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 <output name="sabund" file="amazon.an.sabund2" ftype="mothur.sabund"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 <expand macro="logfile-test"/>
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49 </test>
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50 <test><!-- test otu list input -->
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51 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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52 <param name="label" value="0.03,0.05"/>
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 <output name="sabund" file="amazon.an.sabund3" ftype="mothur.sabund"/>
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54 <expand macro="logfile-test"/>
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55 </test>
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56 </tests>
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57 <help>
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58 <![CDATA[
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59
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60 @MOTHUR_OVERVIEW@
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61
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62
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63 **Command Documentation**
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64
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65 The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file.
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66
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67 .. _sabund: https://www.mothur.org/wiki/Sabund_file
579ffc8e2b4b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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68 .. _list: https://www.mothur.org/wiki/List_file
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69 .. _rabund: https://www.mothur.org/wiki/Rabund_file
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70 .. _get.sabund: https://www.mothur.org/wiki/Get.sabund
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71
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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>