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