Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/chimera.check.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_check" name="Chimera.check" version="1.16.0" force_history_refresh="True"> | 1 <tool id="mothur_chimera_check" name="Chimera.check" version="1.19.0" force_history_refresh="True"> |
2 <description>Find putative chimeras using chimeraCheck</description> | 2 <description>Find putative chimeras using chimeraCheck</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='chimera.check' | 5 --cmd='chimera.check' |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.chimeracheck\.chimeras$:'$out_file | 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.chimeracheck\.chimeras$:'$out_file |
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 #if int($ksize.__str__) > 0: | 10 #if int($ksize.__str__) > 0: |
11 --ksize=$ksize | 11 --ksize=$ksize |
12 #end if | 12 #end if |
13 #if int($increment.__str__) > 0: | 13 #if int($increment.__str__) > 0: |
14 --increment=$increment | 14 --increment=$increment |
15 #end if | 15 #end if |
16 #if $svg.gen == 'yes': | 16 #if $svg.gen == 'yes': |
17 --svg=true | 17 --svg=true |
18 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' | 18 #if $svg.name.__str__ != "None" and len($svg.name.__str__) > 0: |
19 --new_datasets='^(\S+)\.chimeracheck\.svg$:svg' | 19 --name='$svg.name' |
20 #if $name.__str__ != "None" and len($name.__str__) > 0: | 20 #end if |
21 --name='$name' | 21 #if $svg.as_datasets.__str__ == "yes": |
22 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' | |
23 --new_datasets='^(\S+)\.chimeracheck\.svg$:svg' | |
22 #end if | 24 #end if |
23 #end if | 25 #end if |
24 --processors=2 | 26 --processors=2 |
25 </command> | 27 </command> |
26 <inputs> | 28 <inputs> |
27 <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> | 29 <param name="fasta" type="data" format="align" label="fasta - Candiate Aligned Sequences"/> |
28 <conditional name="alignment"> | 30 <conditional name="alignment"> |
29 <param name="source" type="select" label="Select Template from" help=""> | 31 <param name="source" type="select" label="Select Reference Template from" help=""> |
30 <option value="hist">History</option> | 32 <option value="hist">History</option> |
31 <option value="ref">Cached Reference</option> | 33 <option value="ref">Cached Reference</option> |
32 </param> | 34 </param> |
33 <when value="ref"> | 35 <when value="ref"> |
34 <param name="template" type="select" label="template - Select an alignment database " help=""> | 36 <param name="template" type="select" label="reference - Select an alignment database " help=""> |
35 <options from_file="mothur_aligndb.loc"> | 37 <options from_file="mothur_aligndb.loc"> |
36 <column name="name" index="0" /> | 38 <column name="name" index="0" /> |
37 <column name="value" index="1" /> | 39 <column name="value" index="1" /> |
38 </options> | 40 </options> |
39 </param> | 41 </param> |
40 </when> | 42 </when> |
41 <when value="hist"> | 43 <when value="hist"> |
42 <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/> | 44 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/> |
43 </when> | 45 </when> |
44 </conditional> | 46 </conditional> |
45 <param name="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments (uses default if < 1)"/> | 47 <param name="ksize" type="integer" value="7" label="ksize - kmer length to determine differences between sequence fragments (uses default if < 1)"/> |
46 <param name="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration (uses default if < 1)" | 48 <param name="increment" type="integer" value="10" label="increment - Increment for window slide on each iteration (uses default if < 1)" |
47 help="Default is 10, but you may set it up to sequence length minus twice the window."/> | 49 help="Default is 10, but you may set it up to sequence length minus twice the window."/> |
51 <option value="yes">Yes</option> | 53 <option value="yes">Yes</option> |
52 </param> | 54 </param> |
53 <when value="no"/> | 55 <when value="no"/> |
54 <when value="yes"> | 56 <when value="yes"> |
55 <param name="name" type="data" format="names" optional="true" label="name - Names of queries for which to generate SVG plot"/> | 57 <param name="name" type="data" format="names" optional="true" label="name - Names of queries for which to generate SVG plot"/> |
58 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/> | |
56 </when> | 59 </when> |
57 </conditional> | 60 </conditional> |
58 </inputs> | 61 </inputs> |
59 <outputs> | 62 <outputs> |
60 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 63 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
74 | 77 |
75 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 78 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
76 | 79 |
77 **Command Documenation** | 80 **Command Documenation** |
78 | 81 |
79 The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced. | 82 The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows. |
83 | |
84 Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced. | |
80 | 85 |
81 .. _chimera.check: http://www.mothur.org/wiki/Chimera.check | 86 .. _chimera.check: http://www.mothur.org/wiki/Chimera.check |
82 | 87 |
83 | 88 |
84 </help> | 89 </help> |