Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/sffinfo.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_sffinfo" name="Sffinfo" version="1.15.0"> | |
2 <description>Summarize the quality of sequences</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 --cmd='sffinfo' | |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fasta$:'$out_fasta,'^\S+\.qual$:'$out_qfile,'^\S+\.sff\.txt$:'$out_sfftxt,'^\S+\.flow$:'$out_flow | |
7 --outputdir='$logfile.extra_files_path' | |
8 --sff=$sff | |
9 $fasta | |
10 $qfile | |
11 $sfftxt | |
12 $flow | |
13 $trim | |
14 #if $accnos.__str__ != 'None' and len($accnos.__str__) > 0: | |
15 --accnos=$accnos | |
16 #end if | |
17 </command> | |
18 <inputs> | |
19 <param name="sff" type="data" format="sff" label="sff - Sff data"/> | |
20 <!-- | |
21 <repeat name="more" title="Additional "> | |
22 <param name="sff" type="data" format="sff" label="sff - Sff data"/> | |
23 </repeat> | |
24 --> | |
25 <!-- | |
26 <param name="datasets" type="select" display="checkboxes" multiple="True" label="datasets - Choose output files for your history" help="Selected outputs will be listed as datasets in your history"> | |
27 <option value="fasta">fasta</option> | |
28 <option value="qfile">qfile</option> | |
29 <option value="sfftxt">sfftxt</option> | |
30 <option value="flow">flow</option> | |
31 </param> | |
32 --> | |
33 <param name="fasta" type="boolean" truevalue="" falsevalue="--fasta=false" checked="true" label="fasta - Add fasta to your history" /> | |
34 <param name="qfile" type="boolean" truevalue="" falsevalue="--qfile=false" checked="true" label="qfile - Add qfile to your history" /> | |
35 <param name="sfftxt" type="boolean" truevalue="--sfftxt=true" falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history" /> | |
36 <param name="flow" type="boolean" truevalue="--flow=true" falsevalue="" checked="false" label="flow - Add flow to your history" /> | |
37 <param name="trim" type="boolean" truevalue="" falsevalue="--trim=false" checked="true" label="trim - Trim sequences and quality scores" /> | |
38 <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Limit output to named Accessions"/> | |
39 </inputs> | |
40 <outputs> | |
41 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
42 <data format="fasta" name="out_fasta" label="${tool.name} on ${on_string}: fasta"> | |
43 <filter>fasta == True</filter> | |
44 </data> | |
45 <data format="qual454" name="out_qfile" label="${tool.name} on ${on_string}: qual"> | |
46 <filter>qfile == True</filter> | |
47 </data> | |
48 <data format="txt" name="out_sfftxt" label="${tool.name} on ${on_string}: sff.txt"> | |
49 <filter>sfftxt == True</filter> | |
50 </data> | |
51 <data format="txt" name="out_flow" label="${tool.name} on ${on_string}: flowgram"> | |
52 <filter>flow == True</filter> | |
53 </data> | |
54 </outputs> | |
55 <requirements> | |
56 <requirement type="binary">mothur</requirement> | |
57 </requirements> | |
58 <tests> | |
59 </tests> | |
60 <help> | |
61 **Mothur Overview** | |
62 | |
63 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
64 in the Department of Microbiology and Immunology at The University of Michigan, | |
65 provides bioinformatics for the microbial ecology community. | |
66 | |
67 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
68 | |
69 **Command Documenation** | |
70 | |
71 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file. | |
72 | |
73 | |
74 .. _sffinfo: http://www.mothur.org/wiki/Sffinfo | |
75 | |
76 </help> | |
77 </tool> |