Mercurial > repos > iuc > mothur_get_label

annotate get.label.xml @ 1:83cf3f511e72 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:12:03 -0400
parents 8dd86660e447
children 6d082f402534
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8dd86660e447 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_label" name="Get.label" version="@WRAPPER_VERSION@.0">
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>label names from list, sabund, or rabund file</description>
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3 <macros>
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4 <import>macros.xml</import>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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
0
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ## create symlinks to input datasets
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$otu" otu.dat &&
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 echo 'get.label(
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #if $otu.is_of_type("mothur.rabund"):
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17 rabund=otu.dat
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #elif $otu.is_of_type("mothur.sabund"):
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 sabund=otu.dat
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20 #else
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 list=otu.dat
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #end if
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 )'
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 | sed 's/ //g' ## mothur trips over whitespace
1
83cf3f511e72 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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25 | mothur
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26 | tee mothur.out.log &&
0
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 ## parse relevant output from logfile to file
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 cat mothur.*.logfile
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 | head -n-3
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31 | sed '1,29d'
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 > "$labels_list"
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 ]]></command>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <inputs>
8dd86660e447 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,motur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 </inputs>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <outputs>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <expand macro="logfile-output"/>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <data name="labels_list" format="tabular" label="${tool.name} on ${on_string}: labels"/>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 </outputs>
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41 <tests>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <test><!-- test with sabund -->
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <expand macro="logfile-test"/>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 </test>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <test><!-- test with rabund -->
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <param name="otu" value="amazon.an.rabund2" ftype="mothur.rabund"/>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <output name="labels_list" md5="0c3fab5bdfa8588c7244048ddd4eac3c" ftype="tabular"/>
8dd86660e447 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"/>
8dd86660e447 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 </test>
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52 <test><!-- test with list -->
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53 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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54 <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
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55 <expand macro="logfile-test"/>
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56 </test>
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57 </tests>
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58 <help>
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59 <![CDATA[
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60
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61 @MOTHUR_OVERVIEW@
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62
1
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63 **Command Documentation**
0
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64
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65 The get.label_ command generate principle components plot data.
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66
1
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67 .. _get.label: https://www.mothur.org/wiki/Get.label
0
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68
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69 v.1.20.0: Updated to Mothur 1.33
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70 ]]>
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71 </help>
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72 <expand macro="citations"/>
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73 </tool>