Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/dist.seqs.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
parents | |
children | fcc0778f6987 |
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1 <tool id="mothur_dist_seqs" name="Dist.seqs" version="1.15.0"> | |
2 <description>calculate uncorrected pairwise distances between aligned sequences</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 --cmd='dist.seqs' | |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.dist$:'$out_dist | |
7 --outputdir='$logfile.extra_files_path' | |
8 --fasta=$fasta | |
9 #if len($calc.__str__) > 0: | |
10 --calc=$calc | |
11 #end if | |
12 $countends | |
13 #if float($cutoff.__str__) > 0.0: | |
14 --cutoff=$cutoff | |
15 #end if | |
16 #if len($output.__str__) > 0: | |
17 --output=$output | |
18 #end if | |
19 </command> | |
20 <inputs> | |
21 <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/> | |
22 <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help=""> | |
23 <option value="">use default</option> | |
24 <option value="onegap">onegap - counts a string of gaps as a single gap</option> | |
25 <option value="nogaps">nogaps - ignores gaps</option> | |
26 <option value="eachgap ">eachgap - penalize each gap</option> | |
27 </param> | |
28 <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="--countends=false" label="countends - Penalize terminal gaps"/> | |
29 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" | |
30 help="Do not save any distances larger than this, a common value would be 0.10"/> | |
31 <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> | |
32 <option value="">Default Column-Formatted Matrix</option> | |
33 <option value="lt">Phylip formatted Lower Triangle Matrix</option> | |
34 <option value="square">Phylip formatted Square Matrix</option> | |
35 </param> | |
36 <!-- | |
37 oldfasta | |
38 column | |
39 --> | |
40 </inputs> | |
41 <outputs> | |
42 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
43 <data format="pair.dist" name="out_dist" label="${tool.name} on ${on_string}: dist"> | |
44 <change_format> | |
45 <when input="output" value="lt" format="lower.dist" /> | |
46 <when input="output" value="square" format="square.dist" /> | |
47 </change_format> | |
48 </data> | |
49 </outputs> | |
50 <requirements> | |
51 <requirement type="binary">mothur</requirement> | |
52 </requirements> | |
53 <tests> | |
54 </tests> | |
55 <help> | |
56 **Mothur Overview** | |
57 | |
58 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
59 in the Department of Microbiology and Immunology at The University of Michigan, | |
60 provides bioinformatics for the microbial ecology community. | |
61 | |
62 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
63 | |
64 **Command Documenation** | |
65 | |
66 The dist.seqs_ command will calculate uncorrected pairwise distances between aligned sequences. | |
67 | |
68 .. _dist.seqs: http://www.mothur.org/wiki/Dist.seqs | |
69 | |
70 | |
71 </help> | |
72 </tool> |