Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/chimera.perseus.xml @ 18:697156806162
Mothur - update for Mothur version 1.23.0
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 17 Jan 2012 11:22:44 -0600 |
parents | |
children | 49058b1f8d3f |
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1 <tool id="mothur_chimera_perseus" name="Chimera.perseus" version="1.23.0" > | |
2 <description>Find putative chimeras using chimeraCheck</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 --cmd='chimera.perseus' | |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.perseus\.chimeras?$:'$out_file | |
7 --outputdir='$logfile.extra_files_path' | |
8 --fasta=$fasta | |
9 --name=$name | |
10 #if $group.__str__ != "None" and len($group.__str__) > 0: | |
11 --group='$group' | |
12 #end if | |
13 #if $alpha.__str__ != '': | |
14 --alpha=$alpha | |
15 #end if | |
16 #if $beta.__str__ != '': | |
17 --beta=$beta | |
18 #end if | |
19 #if $cutoff.__str__ != '': | |
20 --cutoff=$cutoff | |
21 #end if | |
22 --processors=8 | |
23 </command> | |
24 <inputs> | |
25 <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/> | |
26 <param name="name" type="data" format="names" label="name - Names "/> | |
27 <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> | |
28 <param name="alpha" type="float" value="-5.54" optional="true" label="alpha" help="The default is -5.54"/> | |
29 <param name="beta" type="float" value="0.33" optional="true" label="beta" help="The default is 0.33"/> | |
30 <param name="cutoff" type="float" value="0.50" optional="true" label="cutoff" help="The default is 0.50"/> | |
31 </inputs> | |
32 <outputs> | |
33 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
34 <data format="tabular" name="out_file" label="${tool.name} on ${on_string}: perseus.chimeras" /> | |
35 </outputs> | |
36 <requirements> | |
37 <requirement type="binary">mothur</requirement> | |
38 </requirements> | |
39 <tests> | |
40 </tests> | |
41 <help> | |
42 **Mothur Overview** | |
43 | |
44 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
45 in the Department of Microbiology and Immunology at The University of Michigan, | |
46 provides bioinformatics for the microbial ecology community. | |
47 | |
48 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
49 | |
50 **Command Documenation** | |
51 | |
52 The chimera.perseus_ command reads a fasta and name file, and outputs potentially chimeric sequences. | |
53 | |
54 .. _chimera.perseus: http://www.mothur.org/wiki/Chimera.perseus | |
55 | |
56 | |
57 </help> | |
58 </tool> |