Mercurial > repos > iuc > mothur_classify_tree

annotate classify.tree.xml @ 0:2acbb5457141 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 17:37:15 -0400
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2acbb5457141 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_classify_tree" name="Classify.tree" version="@WRAPPER_VERSION@.0">
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2 <description>Get a consensus taxonomy for each node on a tree</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
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10 ln -s "$tree" tree.dat &&
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11 ln -s "$name" name.dat &&
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$group" group.dat &&
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$taxonomy" taxonomy.dat &&
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14
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15 echo 'classify.tree(
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 tree=tree.dat,
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17 #if $name
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18 name=name.dat,
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19 #end if
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20 #if $group:
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21 group=group.dat,
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22 #end if
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23 taxonomy=taxonomy.dat
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24 )'
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 | sed 's/ //g' ## mothur trips over whitespace
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 | mothur
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27 ]]></command>
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28 <inputs>
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29 <param name="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 <param name="tree" type="data" format="txt" label="tree - Sequences to filter"/>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <param name="group" type="data" format="group" optional="true" label="group - Sequences Group reference"/>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <param name="cutoff" type="integer" value="51" min="51" max="100" optional="true" label="cutoff - consensus confidence threshold" help="The default is 51, meaning 51%. Cutoff cannot be below 51"/>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 </inputs>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <outputs>
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36 <expand macro="logfile-output"/>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <data name="out_tree" format="txt" from_work_dir="tree.*taxonomy.tre" label="${tool.name} on ${on_string}: taxonomy.tre"/>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <data name="summary" format="tabular" from_work_dir="tree.*taxonomy.summary" label="${tool.name} on ${on_string}: taxonomy.summary"/>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 </outputs>
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40 <tests>
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41 <test>
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42 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.ref.taxonomy"/>
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43 <param name="tree" value="treetest.tre" ftype="txt"/>
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44 <output name="out_tree" md5="cd2d3275d225ee8ba5df004a9885f50c" ftype="txt"/>
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45 <output name="summary" md5="78dfe4198793f7ee5632c5b88b6bc295" ftype="tabular"/>
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46 <expand macro="logfile-test"/>
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47 </test>
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48 </tests>
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49 <help>
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50 <![CDATA[
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51
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52 @MOTHUR_OVERVIEW@
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53
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54
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55 **Command Documenation**
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56
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57 The classify.tree_ command is used to get a consensus taxonomy for each node on a tree.
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58 Input is a taxonomy_ and a tree_ with optional name_ or group_ reference.
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59 The output is a tree_ and a summary..
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60
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61 TreeNode NumRep Taxonomy
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62 243 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
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63 244 3 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
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64 245 4 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
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65 ...
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66
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67
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68 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
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69 .. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html
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70 .. _name: http://www.mothur.org/wiki/Name_file
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71 .. _group: http://www.mothur.org/wiki/Group_file
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72 .. _classify.tree: http://www.mothur.org/wiki/Classify.tree
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73
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74 v.1.25.0: Trivial upgrade to Mothur 1.33
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75 ]]>
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76 </help>
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77 <expand macro="citations"/>
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78 </tool>