Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/chimera.ccode.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 | fcc0778f6987 |
children | ce6e81622c6a |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.16.0"> | 1 <tool id="mothur_chimera_ccode" name="Chimera.ccode" version="1.19.0"> |
2 <description>Find putative chimeras using ccode</description> | 2 <description>Find putative chimeras using ccode</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='chimera.ccode' | 5 --cmd='chimera.ccode' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.ccode\.chimeras$:'$out_file,'^\S+\.ccode\.accnos$:'$out_accnos | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.ccode\.chimeras$:'$out_file,'^\S+\.ccode\.accnos$:'$out_accnos |
7 --outputdir='$logfile.extra_files_path' | 7 --outputdir='$logfile.extra_files_path' |
8 --fasta=$fasta | 8 --fasta=$fasta |
9 --template=$alignment.template | 9 --reference=$alignment.template |
10 $filter | 10 $filter |
11 #if $mask.source == 'default': | 11 #if $mask.source == 'default': |
12 --mask=default | 12 --mask=default |
13 #elif $mask.source == 'history': | 13 #elif $mask.source == 'history': |
14 --mask=$mask.input | 14 --mask=$mask.input |
20 --numwanted=$numwanted | 20 --numwanted=$numwanted |
21 #end if | 21 #end if |
22 --processors=2 | 22 --processors=2 |
23 </command> | 23 </command> |
24 <inputs> | 24 <inputs> |
25 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> | 25 <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/> |
26 <conditional name="alignment"> | 26 <conditional name="alignment"> |
27 <param name="source" type="select" label="Select Template from" help=""> | 27 <param name="source" type="select" label="Select Reference Template from" help=""> |
28 <option value="hist">History</option> | 28 <option value="hist">History</option> |
29 <option value="ref">Cached Reference</option> | 29 <option value="ref">Cached Reference</option> |
30 </param> | 30 </param> |
31 <when value="ref"> | 31 <when value="ref"> |
32 <param name="template" type="select" label="template - Select an alignment database " help=""> | 32 <param name="template" type="select" label="reference - Select an alignment database " help=""> |
33 <options from_file="mothur_aligndb.loc"> | 33 <options from_file="mothur_aligndb.loc"> |
34 <column name="name" index="0" /> | 34 <column name="name" index="0" /> |
35 <column name="value" index="1" /> | 35 <column name="value" index="1" /> |
36 </options> | 36 </options> |
37 </param> | 37 </param> |
38 </when> | 38 </when> |
39 <when value="hist"> | 39 <when value="hist"> |
40 <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/> | 40 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> |
41 </when> | 41 </when> |
42 </conditional> | 42 </conditional> |
43 <param name="filter" type="boolean" falsevalue="" truevalue="--filter=true" checked="false" label="filter - Apply a 50% soft vertical filter"/> | 43 <param name="filter" type="boolean" falsevalue="" truevalue="--filter=true" checked="false" label="filter - Apply a 50% soft vertical filter"/> |
44 <!-- mask --> | 44 <!-- mask --> |
45 <conditional name="mask"> | 45 <conditional name="mask"> |
46 <param name="source" type="select" label="Mask option"> | 46 <param name="source" type="select" label="Mask option"> |
47 <option value="">None</option> | 47 <option value="">None</option> |
48 <option value="default">default ecoli mask</option> | 48 <option value="default">default ecoli mask</option> |
49 <option value="history">From your history</option> | 49 <option value="history">From Your History</option> |
50 </param> | 50 </param> |
51 <when value=""/> | 51 <when value=""/> |
52 <when value="default"/> | 52 <when value="default"/> |
53 <when value="history"> | 53 <when value="history"> |
54 <param name="input" type="data" format="filter" label="Mask for the template file" help=""/> | 54 <param name="input" type="data" format="filter" label="Mask for the reference file" help=""/> |
55 </when> | 55 </when> |
56 </conditional> | 56 </conditional> |
57 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if < 1)" | 57 <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (default if < 1)" |
58 help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/> | 58 help="Recommended window size is between 5 and 20% of your trimmed sequence length. Default is 10% of the sequence length."/> |
59 <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/> | 59 <param name="numwanted" type="integer" value="20" label="numwanted - Number of sequences compared with each query (uses default if set to 0)"/> |
77 | 77 |
78 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 78 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
79 | 79 |
80 **Command Documenation** | 80 **Command Documenation** |
81 | 81 |
82 The chimera.ccode_ command identifies putative chimeras using the ccode approach. | 82 The chimera.ccode_ command identifies putative chimeras using the ccode approach (Chimera and Cross-Over Detection and Evaluation). Ccode_ compares differences in distances, for each word, between query sequence and reference sequences, and reference sequences and themselves. |
83 | 83 |
84 This method was written using the algorithms described in the paper_ "Evaluating putative chimeric sequences from PCR-amplified products" by Juan M. Gonzalez, Johannes Zimmerman and Cesareo Saiz-Jimenez. | |
85 | |
86 The program can analyze sequences for any required word length. Generally, values of 5-20% of sequence length appear to deliver accurate results, for example, working on 16S rDNA sequences with a full-length of #1500 nt. It should be noted that the use of fragments either too long or too short might result in a reduction of sensitivity. | |
87 | |
88 .. _Ccode: http://www.microextreme.net/downloads.html | |
89 .. _paper: http://bioinformatics.oxfordjournals.org/content/21/3/333.full.pdf | |
84 .. _chimera.ccode: http://www.mothur.org/wiki/Chimera.ccode | 90 .. _chimera.ccode: http://www.mothur.org/wiki/Chimera.ccode |
85 | 91 |
86 | 92 |
87 </help> | 93 </help> |
88 </tool> | 94 </tool> |