Mercurial > repos > iuc > mothur_classify_tree

comparison classify.tree.xml @ 1:c51b7f1f7972 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:26:00 -0400
parents 2acbb5457141
children 61b024f58c48
comparison
equal deleted inserted replaced
0:2acbb5457141 1:c51b7f1f7972
2 <description>Get a consensus taxonomy for each node on a tree</description> 2 <description>Get a consensus taxonomy for each node on a tree</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$tree" tree.dat && 13 ln -s "$tree" tree.dat &&
11 ln -s "$name" name.dat && 14 ln -s "$name" name.dat &&
12 ln -s "$group" group.dat && 15 ln -s "$group" group.dat &&
13 ln -s "$taxonomy" taxonomy.dat && 16 ln -s "$taxonomy" taxonomy.dat &&
22 #end if 25 #end if
23 taxonomy=taxonomy.dat 26 taxonomy=taxonomy.dat
24 )' 27 )'
25 | sed 's/ //g' ## mothur trips over whitespace 28 | sed 's/ //g' ## mothur trips over whitespace
26 | mothur 29 | mothur
30 | tee mothur.out.log
27 ]]></command> 31 ]]></command>
28 <inputs> 32 <inputs>
29 <param name="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> 33 <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"/> 34 <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"/> 35 <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file"/>
50 <![CDATA[ 54 <![CDATA[
51 55
52 @MOTHUR_OVERVIEW@ 56 @MOTHUR_OVERVIEW@
53 57
54 58
55 **Command Documenation** 59 **Command Documentation**
56 60
57 The classify.tree_ command is used to get a consensus taxonomy for each node on a tree. 61 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. 62 Input is a taxonomy_ and a tree_ with optional name_ or group_ reference.
59 The output is a tree_ and a summary.. 63 The output is a tree_ and a summary..
60 64
63 244 3 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);
64 245 4 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);
65 ... 69 ...
66 70
67 71
68 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline 72 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
69 .. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html 73 .. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html
70 .. _name: http://www.mothur.org/wiki/Name_file 74 .. _name: https://www.mothur.org/wiki/Name_file
71 .. _group: http://www.mothur.org/wiki/Group_file 75 .. _group: https://www.mothur.org/wiki/Group_file
72 .. _classify.tree: http://www.mothur.org/wiki/Classify.tree 76 .. _classify.tree: https://www.mothur.org/wiki/Classify.tree
73 77
74 v.1.25.0: Trivial upgrade to Mothur 1.33 78 v.1.25.0: Trivial upgrade to Mothur 1.33
75 ]]> 79 ]]>
76 </help> 80 </help>
77 <expand macro="citations"/> 81 <expand macro="citations"/>