Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/chimera.slayer.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_slayer" name="Chimera.slayer" version="1.16.0"> | 1 <tool id="mothur_chimera_slayer" name="Chimera.slayer" version="1.19.0"> |
2 <description>Find putative chimeras using slayer</description> | 2 <description>Find putative chimeras using slayer</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='chimera.slayer' | 5 --cmd='chimera.slayer' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.slayer\.chimeras$:'$out_file,'^\S+\.slayer\.accnos$:'$out_accnos | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.slayer\.chimeras$:'$out_file,'^\S+\.slayer\.accnos$:'$out_accnos |
7 --outputdir='$logfile.extra_files_path' | 7 --outputdir='$logfile.extra_files_path' |
8 --tmpdir='${logfile.extra_files_path}/input' | 8 --tmpdir='${logfile.extra_files_path}/input' |
9 --fasta=$fasta | 9 --fasta=$fasta |
10 #if $alignment.source == 'self': | 10 #if $alignment.source == 'self': |
11 --template='self' | 11 --reference='self' |
12 #if $alignment.name.__str__ != "None" and len($alignment.name.__str__) > 0: | 12 #if $alignment.name.__str__ != "None" and len($alignment.name.__str__) > 0: |
13 --name=$alignment.name | 13 --name=$alignment.name |
14 #end if | 14 #end if |
15 #else: | 15 #else: |
16 --template=$alignment.template | 16 --reference=$alignment.template |
17 #end if | 17 #end if |
18 #if $options.setby == 'user': | 18 #if $options.setby == 'user': |
19 --search=$options.search | 19 --search=$options.search |
20 --window=$options.window | 20 --window=$options.window |
21 --increment=$options.increment | 21 --increment=$options.increment |
28 --iters=$options.iters | 28 --iters=$options.iters |
29 --minbs=$options.minbs | 29 --minbs=$options.minbs |
30 --minsnp=$options.minsnp | 30 --minsnp=$options.minsnp |
31 --divergence=$options.divergence | 31 --divergence=$options.divergence |
32 $options.trim | 32 $options.trim |
33 $options.split | |
33 #end if | 34 #end if |
34 --processors=2 | 35 --processors=2 |
35 </command> | 36 </command> |
36 <inputs> | 37 <inputs> |
37 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> | 38 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> |
38 <conditional name="alignment"> | 39 <conditional name="alignment"> |
39 <param name="source" type="select" label="Select Template from" help=""> | 40 <param name="source" type="select" label="Select Reference Template from" help=""> |
40 <option value="hist">History</option> | 41 <option value="hist">History</option> |
41 <option value="ref">Cached Reference</option> | 42 <option value="ref">Cached Reference</option> |
42 <option value="self">Self - Use abundant sequences from the input Candiate Sequences fasta </option> | 43 <option value="self">Self - Use abundant sequences from the input Candiate Sequences fasta </option> |
43 </param> | 44 </param> |
44 <when value="ref"> | 45 <when value="ref"> |
45 <param name="template" type="select" label="template - Select an alignment database " help=""> | 46 <param name="template" type="select" label="reference - Select an alignment database " help=""> |
46 <options from_file="mothur_aligndb.loc"> | 47 <options from_file="mothur_aligndb.loc"> |
47 <column name="name" index="0" /> | 48 <column name="name" index="0" /> |
48 <column name="value" index="1" /> | 49 <column name="value" index="1" /> |
49 </options> | 50 </options> |
50 </param> | 51 </param> |
51 </when> | 52 </when> |
52 <when value="hist"> | 53 <when value="hist"> |
53 <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/> | 54 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> |
54 </when> | 55 </when> |
55 <when value="self"> | 56 <when value="self"> |
56 <param name="name" type="data" format="names" optional="true" label="names - Sequences Names"/> | 57 <param name="name" type="data" format="names" optional="true" label="names - Sequences Names"/> |
57 </when> | 58 </when> |
58 </conditional> | 59 </conditional> |
73 <param name="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/> | 74 <param name="match" type="integer" value="5" label="match - Reward matched bases (default 5)"/> |
74 <param name="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/> | 75 <param name="mismatch" type="integer" value="-4" label="mismatch - Penalty for mismatched bases (default -4)"/> |
75 <param name="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/> | 76 <param name="numwanted" type="integer" value="15" label="numwanted - Number of potential parents to to compare with query sequence (default 15)"/> |
76 <param name="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/> | 77 <param name="parents" type="integer" value="3" label="parents - Number of potential parents to investigate from the numwanted best matches"/> |
77 <param name="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/> | 78 <param name="minsim" type="integer" value="90" label="minsim - Minimum similarity % between the query and parent (default 90)"/> |
78 <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in template and the query (default 70)"/> | 79 <param name="mincov" type="integer" value="70" label="mincov - Minimum coverage % of closest matches in reference and the query (default 70)"/> |
79 <param name="iters" type="integer" value="100" label="iters - Number of bootstrap iterations to try (default 100)"/> | 80 <param name="iters" type="integer" value="100" label="iters - Number of bootstrap iterations to try (default 100)"/> |
80 <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/> | 81 <param name="minbs" type="integer" value="90" label="minbs - Minimum bootstrap support % for calling a sequence chimeric (default 90)"/> |
81 <param name="minsnp" type="integer" value="100" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/> | 82 <param name="minsnp" type="integer" value="100" label="minsnp - Percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default 100)"/> |
82 <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/> | 83 <param name="divergence" type="float" value="1.007" label="divergence - Divergence cutoff for chimera determination (default 1.007)"/> |
83 <param name="trim" type="boolean" truevalue="--trim=True" falsevalue="" checked="false" label="trim - include chimeric sequences trimmed to their longest peice" /> | 84 <param name="trim" type="boolean" truevalue="--trim=True" falsevalue="" checked="false" label="trim - include chimeric sequences trimmed to their longest peice" /> |
85 <param name="split" type="boolean" truevalue="--split=True" falsevalue="" checked="false" label="split - detect tri- and quadmeras" help="if a sequence comes back as non-chimeric, mothur will test the two sides to see if they are chimeric."/> | |
84 </when> | 86 </when> |
85 </conditional> | 87 </conditional> |
86 </inputs> | 88 </inputs> |
87 <outputs> | 89 <outputs> |
88 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 90 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
105 | 107 |
106 **Command Documenation** | 108 **Command Documenation** |
107 | 109 |
108 The chimera.slayer_ command identifies putative chimeras using the slayer approach. | 110 The chimera.slayer_ command identifies putative chimeras using the slayer approach. |
109 | 111 |
112 ChimeraSlayer_ is a chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | |
113 | |
114 Chimera Slayer involves the following series of steps that operate to flag chimeric 16S rRNA sequences: | |
115 | |
116 (A) the ends of a query sequence are searched against an included database of reference chimera-free 16S sequences to identify potential parents of a chimera; | |
117 (B) candidate parents of a chimera are selected as those that form a branched best scoring alignment to the NAST-formatted query sequence; | |
118 (C) the NAST alignment of the query sequence is improved in a `chimera-aware' profile-based NAST realignment to the selected reference parent sequences; and | |
119 (D) an evolutionary framework is used to flag query sequences found to exhibit greater sequence homology to an in silico chimera formed between any two of the selected reference parent sequences. | |
120 | |
121 Note: | |
122 It is not recommended to blindly discard all sequences flagged as chimeras. Some may represent naturally formed chimeras that do not represent PCR artifacts. Sequences flagged may warrant further investigation. | |
123 | |
124 | |
125 .. _ChimeraSlayer: http://microbiomeutil.sourceforge.net/ | |
110 .. _chimera.slayer: http://www.mothur.org/wiki/Chimera.slayer | 126 .. _chimera.slayer: http://www.mothur.org/wiki/Chimera.slayer |
111 | 127 |
112 | 128 |
113 </help> | 129 </help> |
114 </tool> | 130 </tool> |