Mercurial > repos > iuc > mothur_classify_tree

annotate classify.tree.xml @ 6:f350dab14d28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
author iuc
date Tue, 20 Mar 2018 13:55:11 -0400
parents b48b0dd9b75e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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="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 '$tree' tree.dat &&
b48b0dd9b75e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$name' name.dat &&
b48b0dd9b75e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s '$group' group.dat &&
b48b0dd9b75e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 ln -s '$taxonomy' taxonomy.dat &&
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17
4
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18 echo 'classify.tree(
b48b0dd9b75e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 tree=tree.dat,
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20 #if $name
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21 name=name.dat,
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22 #end if
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23 #if $group:
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24 group=group.dat,
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25 #end if
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26 taxonomy=taxonomy.dat
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27 )'
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28 | sed 's/ //g' ## mothur trips over whitespace
b48b0dd9b75e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 | mothur
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30 | tee mothur.out.log
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31 ]]></command>
2acbb5457141 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <inputs>
4
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33 <param argument="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
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34 <param argument="tree" type="data" format="txt" label="tree - Sequences to filter"/>
b48b0dd9b75e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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35 <param argument="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/>
b48b0dd9b75e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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36 <param argument="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Group reference"/>
b48b0dd9b75e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 <param argument="cutoff" type="integer" value="51" min="51" max="100" optional="true" label="cutoff - consensus confidence threshold"
b48b0dd9b75e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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38 help="The default is 51, meaning 51%. Cutoff cannot be below 51"/>
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39 <expand macro="param-savelog"/>
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40 </inputs>
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41 <outputs>
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42 <expand macro="logfile-output"/>
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43 <data name="out_tree" format="txt" from_work_dir="tree.*taxonomy.tre" label="${tool.name} on ${on_string}: taxonomy.tre"/>
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44 <data name="summary" format="tabular" from_work_dir="tree.*taxonomy.summary" label="${tool.name} on ${on_string}: taxonomy.summary"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.ref.taxonomy"/>
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49 <param name="tree" value="treetest.tre" ftype="txt"/>
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50 <output name="out_tree" md5="cd2d3275d225ee8ba5df004a9885f50c" ftype="txt"/>
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51 <output name="summary" md5="78dfe4198793f7ee5632c5b88b6bc295" ftype="tabular"/>
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52 <param name="savelog" value="true"/>
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53 <expand macro="logfile-test"/>
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54 </test>
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55 </tests>
4
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56 <help><![CDATA[
0
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57
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58 @MOTHUR_OVERVIEW@
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59
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60
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61 **Command Documentation**
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62
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63 The classify.tree_ command is used to get a consensus taxonomy for each node on a tree.
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64 Input is a taxonomy_ and a tree_ with optional name_ or group_ reference.
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65 The output is a tree_ and a summary..
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66
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67 TreeNode NumRep Taxonomy
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68 243 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
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69 244 3 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
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70 245 4 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
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71 ...
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72
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73
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74 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
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75 .. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html
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76 .. _name: https://www.mothur.org/wiki/Name_file
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77 .. _group: https://www.mothur.org/wiki/Group_file
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78 .. _classify.tree: https://www.mothur.org/wiki/Classify.tree
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79
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80 v.1.25.0: Trivial upgrade to Mothur 1.33
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81
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82 ]]></help>
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83 <expand macro="citations"/>
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84 </tool>