annotate phylotype.xml @ 1:e18d25fb125e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author iuc
date Tue, 05 Sep 2017 17:12:52 -0400
parents 61cfe849101c
children f750e0c2c7f9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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61cfe849101c 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_phylotype" name="Phylotype" version="@WRAPPER_VERSION@.0">
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2 <description>Assign sequences to OTUs based on taxonomy</description>
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3 <macros>
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4 <import>macros.xml</import>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
61cfe849101c 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"/>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$taxonomy" taxonomy.dat &&
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$name" name.dat &&
61cfe849101c 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 'phylotype(
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17 taxonomy=taxonomy.dat
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18 #if $cutoff:
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19 ,cutoff=$cutoff
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20 #end if
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 #if $name:
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22 ,name=name.dat
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23 #end if
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24 #if $label:
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25 ,label=${ str($label).replace(",","-") }
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 #end if
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27 )'
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28 | sed 's/ //g' ## mothur trips over whitespace
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29 | mothur
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30 | tee mothur.out.log
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 ]]></command>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 <inputs>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/>
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34 <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/>
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35 <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true">
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36 <option value="0">0</option>
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37 <option value="1">1</option>
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38 <option value="2">2</option>
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39 <option value="3">3</option>
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40 <option value="4">4</option>
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41 <option value="5">5</option>
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42 <option value="6">6</option>
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43 <option value="7">7</option>
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44 <option value="8">8</option>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 <option value="9">9</option>
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46 <option value="10">10</option>
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47 </param>
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48 <param name="cutoff" type="integer" value="" min="0" max="50" optional="true" label="cutoff - Truncate the taxonomy at depth (Ignored if &lt; 0)"/>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 </inputs>
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50 <outputs>
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51 <expand macro="logfile-output"/>
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52 <data name="rabund" format="mothur.rabund" from_work_dir="taxonomy*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
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53 <data name="sabund" format="mothur.sabund" from_work_dir="taxonomy*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
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54 <data name="otulist" format="mothur.list" from_work_dir="taxonomy*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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59 <output name="rabund" md5="689fb6fd2fb4cd0740fc8b62d7e05556" ftype="mothur.rabund"/>
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60 <output name="sabund" md5="62547e84f1d051a16937715433f3d78a" ftype="mothur.sabund"/>
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61 <output name="otulist" md5="c808112d524863bbc973dd721ba18a06" ftype="mothur.list"/>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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62 <expand macro="logfile-test"/>
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63 </test>
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64 <test>
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65 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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66 <param name="label" value="1,4,5"/>
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67 <param name="cutoff" value="5"/>
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68 <output name="rabund" md5="3d2e3821bef6ecd7eaf0ea62e8692154" ftype="mothur.rabund"/>
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69 <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/>
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70 <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/>
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71 <expand macro="logfile-test"/>
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72 </test>
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73 </tests>
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74 <help>
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75 <![CDATA[
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76
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77 @MOTHUR_OVERVIEW@
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78
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79 **Command Documentation**
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80
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81 The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.
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82
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83 .. _list: https://www.mothur.org/wiki/List_file
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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84 .. _rabund: https://www.mothur.org/wiki/Rabund_file
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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85 .. _sabund: https://www.mothur.org/wiki/Sabund_file
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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86 .. _phylotype: https://www.mothur.org/wiki/Phylotype
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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88 ]]>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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89 </help>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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90 <expand macro="citations"/>
61cfe849101c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 </tool>