Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/otu.hierarchy.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | |
children | 370b3fc4e7d3 |
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1 <tool id="mothur_otu_hierarchy" name="Otu.hierarchy" version="1.19.0"> | |
2 <description>Relate OTUs at different distances</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list | |
6 #import re, os.path | |
7 --cmd='otu.hierarchy' | |
8 --outputdir='$logfile.extra_files_path' | |
9 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.otu\.hierarchy$:'$hierarchy | |
10 --list=$list | |
11 --label=$label1,$label2 | |
12 --output=$output | |
13 </command> | |
14 <inputs> | |
15 <param name="list" type="data" format="list" label="list - OTU List"/> | |
16 <param name="label1" type="select" label="label - OTU Label 1" > | |
17 <options from_dataset="list"> | |
18 <column name="name" index="0"/> | |
19 <column name="value" index="0"/> | |
20 </options> | |
21 </param> | |
22 <param name="label2" type="select" label="label - OTU Label 2" help="Must be different than Label 1"> | |
23 <options from_dataset="list"> | |
24 <column name="name" index="0"/> | |
25 <column name="value" index="0"/> | |
26 <filter type="param_value" ref="label1" column="value" keep="false"/> | |
27 </options> | |
28 </param> | |
29 <param name="output" type="select" optional="true" label="output - display the names of the sequences in the otus or the otu numbers"> | |
30 <option value="name" selected="treu">OTU sequence names</option> | |
31 <option value="number">OTU numbers</option> | |
32 </param> | |
33 </inputs> | |
34 <outputs> | |
35 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
36 <data format="tabular" name="hierarchy" label="${tool.name} on ${on_string}: otu.hierarchy"/> | |
37 </outputs> | |
38 <requirements> | |
39 <requirement type="binary">mothur</requirement> | |
40 </requirements> | |
41 <tests> | |
42 </tests> | |
43 <help> | |
44 **Mothur Overview** | |
45 | |
46 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
47 in the Department of Microbiology and Immunology at The University of Michigan, | |
48 provides bioinformatics for the microbial ecology community. | |
49 | |
50 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
51 | |
52 **Command Documenation** | |
53 | |
54 The otu.hierarchy_ command relates OTUs from a list_ at different distances. | |
55 | |
56 .. _list_file: http://www.mothur.org/wiki/List_file | |
57 .. _otu.hierarchy: http://www.mothur.org/wiki/Otu.hierarchy | |
58 | |
59 | |
60 </help> | |
61 </tool> |