Mercurial > repos > iuc > mothur_classify_svm

annotate classify.svm.xml @ 0:ba0b90285bc0 draft default tip

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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 10:29:38 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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1 <tool profile="16.07" id="mothur_classify_svm" name="Classify.svm" version="@WRAPPER_VERSION@.0">
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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2 <description>description</description>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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3 <macros>
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4 <import>macros.xml</import>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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5 </macros>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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6 <expand macro="requirements"/>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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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
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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12 ## create symlinks to input datasets
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$otu' shared.dat &&
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$design' design.dat &&
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15
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16 echo 'classify.svm(
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17 shared=shared.dat,
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18 design=design.dat
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19 #if $label:
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20 ,label=${ str($label).replace(",","-") }
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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21 #end if
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22 #if $groups:
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23 ,groups=${ str($groups).replace(",","-") }
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 #end if
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25 )'
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26 | sed 's/ //g' ## mothur trips over whitespace
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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27 | mothur
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28 | tee mothur.out.log
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 ]]></command>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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30 <inputs>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 <param argument="shared" name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 <param argument="design" type="data" format="mothur.design" label="design - assigns groups to sets" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 <param argument="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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34 <expand macro="labeloptions"/>
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35 </param>
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36 <param argument="groups" type="select" multiple="true" optional="true" label="groups - Groups filter (uses all groups if none are selected)" help="To filter: select select at least 2 groups">
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 <options>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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38 <filter type="data_meta" ref="otu" key="groups"/>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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39 </options>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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40 </param>
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41 </inputs>
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42 <outputs>
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43 <expand macro="logfile-output"/>
ba0b90285bc0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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44 <data name="summary" format="tabular" from_work_dir="shared.RF*summary" label="${tool.name} on ${on_string}: summary"/>
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45 <data name="misclass-summary" format="tabular" from_work_dir="shared.misclassifications*.summary" label="${tool.name} on ${on_string}: misclassifications summary"/>
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46 </outputs>
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47 <tests>
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48 <test><!-- test with defaults -->
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49 <param name="otu" value="stool.final.opti_mcc.shared" ftype="mothur.shared"/>
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50 <param name="design" value="stool.design"/>
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51 <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
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52 <output name="misclass-summary" ftype="tabular">
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53 <assert_contents>
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54 <has_line_matching expression="Sample\tRF classification\tActual classification"/>
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55 <has_text text="F003D000"/>
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56 <has_text text="F003D150"/>
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57 </assert_contents>
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58 </output>
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59 <expand macro="logfile-test"/>
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60 </test>
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61 <test><!-- test with custom settings -->
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62 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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63 <param name="design" value="toymothur.design2"/>
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64 <param name="label" value="0.03"/>
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65 <param name="groups" value="pasture"/>
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66 <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
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67 <output name="misclass-summary" ftype="tabular">
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68 <assert_contents>
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69 <has_line_matching expression="Sample\tRF classification\tActual classification"/>
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70 <has_text text="F003D000"/>
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71 <not_has_text text="F003D150"/>
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72 </assert_contents>
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73 </output>
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74 <expand macro="logfile-test"/>
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78 @MOTHUR_OVERVIEW@
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79
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80
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81 **Command Documentation**
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82
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83
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84 .. _classify.rf: http://www.mothur.org/wiki/Classify.rf
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85 ]]></help>
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86 <expand macro="citations"/>
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87 </tool>