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comparison classify.tree.xml @ 0:636e98c0966e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:05:16 -0400
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-1:000000000000 0:636e98c0966e
1 <tool profile="16.07" id="mothur_classify_tree" name="Classify.tree" version="@WRAPPER_VERSION@.0">
2 <description>Get a consensus taxonomy for each node on a tree</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$tree" tree.dat &&
14 ln -s "$name" name.dat &&
15 ln -s "$group" group.dat &&
16 ln -s "$taxonomy" taxonomy.dat &&
17
18 echo 'classify.tree(
19 tree=tree.dat,
20 #if $name
21 name=name.dat,
22 #end if
23 #if $group:
24 group=group.dat,
25 #end if
26 taxonomy=taxonomy.dat
27 )'
28 | sed 's/ //g' ## mothur trips over whitespace
29 | mothur
30 | tee mothur.out.log
31 ]]></command>
32 <inputs>
33 <param name="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
34 <param name="tree" type="data" format="txt" label="tree - Sequences to filter"/>
35 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/>
36 <param name="group" type="data" format="group" optional="true" label="group - Sequences Group reference"/>
37 <param name="cutoff" type="integer" value="51" min="51" max="100" optional="true" label="cutoff - consensus confidence threshold" help="The default is 51, meaning 51%. Cutoff cannot be below 51"/>
38 </inputs>
39 <outputs>
40 <expand macro="logfile-output"/>
41 <data name="out_tree" format="txt" from_work_dir="tree.*taxonomy.tre" label="${tool.name} on ${on_string}: taxonomy.tre"/>
42 <data name="summary" format="tabular" from_work_dir="tree.*taxonomy.summary" label="${tool.name} on ${on_string}: taxonomy.summary"/>
43 </outputs>
44 <tests>
45 <test>
46 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.ref.taxonomy"/>
47 <param name="tree" value="treetest.tre" ftype="txt"/>
48 <output name="out_tree" md5="cd2d3275d225ee8ba5df004a9885f50c" ftype="txt"/>
49 <output name="summary" md5="78dfe4198793f7ee5632c5b88b6bc295" ftype="tabular"/>
50 <expand macro="logfile-test"/>
51 </test>
52 </tests>
53 <help>
54 <![CDATA[
55
56 @MOTHUR_OVERVIEW@
57
58
59 **Command Documentation**
60
61 The classify.tree_ command is used to get a consensus taxonomy for each node on a tree.
62 Input is a taxonomy_ and a tree_ with optional name_ or group_ reference.
63 The output is a tree_ and a summary..
64
65 TreeNode NumRep Taxonomy
66 243 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
67 244 3 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
68 245 4 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100);
69 ...
70
71
72 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
73 .. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html
74 .. _name: https://www.mothur.org/wiki/Name_file
75 .. _group: https://www.mothur.org/wiki/Group_file
76 .. _classify.tree: https://www.mothur.org/wiki/Classify.tree
77
78 v.1.25.0: Trivial upgrade to Mothur 1.33
79 ]]>
80 </help>
81 <expand macro="citations"/>
82 </tool>