Mercurial > repos > iuc > mothur_get_label

annotate get.label.xml @ 4:2db0ca9ce0d9 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 09:26:19 -0500
parents 6d082f402534
children 5d5df87a14d5
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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>
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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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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 &&
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14
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15 echo 'get.label(
2db0ca9ce0d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 #if $otu.is_of_type("mothur.rabund"):
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17 rabund=otu.dat
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18 #elif $otu.is_of_type("mothur.sabund"):
2db0ca9ce0d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 sabund=otu.dat
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20 #else
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21 list=otu.dat
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22 #end if
2db0ca9ce0d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 )'
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24 | sed 's/ //g' ## mothur trips over whitespace
2db0ca9ce0d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 | mothur
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26 | tee mothur.out.log &&
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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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27
4
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28 ## parse relevant output from logfile to file
2db0ca9ce0d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 cat mothur.*.logfile
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30 | head -n-3
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31 | sed '1,30d'
2db0ca9ce0d9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 > '$labels_list'
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33 ]]></command>
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34 <inputs>
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35 <param name="otu" type="data" format="mothur.list,mothur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/>
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36 </inputs>
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37 <outputs>
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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>
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42 <test><!-- test with sabund -->
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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"/>
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45 <expand macro="logfile-test"/>
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46 </test>
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47 <test><!-- test with rabund -->
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48 <param name="otu" value="amazon.an.rabund2" ftype="mothur.rabund"/>
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49 <output name="labels_list" md5="0c3fab5bdfa8588c7244048ddd4eac3c" ftype="tabular"/>
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50 <expand macro="logfile-test"/>
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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>
4
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58 <help><![CDATA[
0
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59
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60 @MOTHUR_OVERVIEW@
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61
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62 **Command Documentation**
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63
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64 The get.label_ command generate principle components plot data.
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65
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66 .. _get.label: https://www.mothur.org/wiki/Get.label
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67
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68 v.1.20.0: Updated to Mothur 1.33
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69
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70 ]]></help>
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71 <expand macro="citations"/>
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72 </tool>