Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/classify.otu.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 | 7bfe1f843858 |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_classify_otu" name="Classify.otu" version="1.16.0" force_history_refresh="True"> | 1 <tool id="mothur_classify_otu" name="Classify.otu" version="1.19.0" force_history_refresh="True"> |
2 <description>Assign sequences to taxonomy</description> | 2 <description>Assign sequences to taxonomy</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='classify.otu' | 5 --cmd='classify.otu' |
6 --result='^mothur.\S+\.logfile$:'$logfile | 6 --result='^mothur.\S+\.logfile$:'$logfile |
7 --outputdir='$logfile.extra_files_path' | 7 --outputdir='$logfile.extra_files_path' |
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' | 8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
9 --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy' | 9 --new_datasets='^\S+?\.(unique|[0-9.]*\.cons\.taxonomy)$:cons.taxonomy','^\S+?\.(unique|[0-9.]*\.cons\.tax\.summary)$:tax.summary' |
10 --list=$otu | 10 --list=$otu |
11 --taxonomy=$tax.taxonomy | 11 --taxonomy=$tax.taxonomy |
12 #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0: | 12 #if $reftax.source != 'none' and len($reftax.taxonomy.__str__) > 0: |
13 --reftaxonomy=$reftax.taxonomy | 13 --reftaxonomy=$reftax.taxonomy |
14 #end if | 14 #end if |
16 --cutoff=$cutoff | 16 --cutoff=$cutoff |
17 #end if | 17 #end if |
18 #if $label.__str__ != "None" and len($label.__str__) > 0: | 18 #if $label.__str__ != "None" and len($label.__str__) > 0: |
19 --label='$label' | 19 --label='$label' |
20 #end if | 20 #end if |
21 #if $group.__str__ != "None" and len($group.__str__) > 0: | |
22 --group='$group' | |
23 #end if | |
24 --basis=$basis | |
21 $probs | 25 $probs |
22 </command> | 26 </command> |
23 <inputs> | 27 <inputs> |
24 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List "/> | 28 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List "/> |
25 <conditional name="tax"> | 29 <conditional name="tax"> |
26 <param name="source" type="select" label="Select Taxonomy from" help=""> | 30 <param name="source" type="select" label="Select Taxonomy from" help=""> |
27 <option value="hist">History</option> | 31 <option value="hist">History</option> |
28 <option value="ref">Cached Reference</option> | 32 <option value="ref">Cached Reference</option> |
29 </param> | 33 </param> |
30 <when value="ref"> | 34 <when value="ref"> |
31 <param name="taxonomy" type="select" format="taxonomy" label="taxonomy - Taxonomy Reference"> | 35 <param name="taxonomy" type="select" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"> |
32 <options from_file="mothur_taxonomy.loc"> | 36 <options from_file="mothur_taxonomy.loc"> |
33 <column name="name" index="0" /> | 37 <column name="name" index="0" /> |
34 <column name="value" index="1" /> | 38 <column name="value" index="1" /> |
35 </options> | 39 </options> |
36 </param> | 40 </param> |
37 </when> | 41 </when> |
38 <when value="hist"> | 42 <when value="hist"> |
39 <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy Reference"/> | 43 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy Reference"/> |
40 </when> | 44 </when> |
41 </conditional> | 45 </conditional> |
42 <conditional name="reftax"> | 46 <conditional name="reftax"> |
43 <param name="source" type="select" label="Select Taxonomy from" help=""> | 47 <param name="source" type="select" label="Select Taxonomy from" help=""> |
44 <option value="none">None</option> | 48 <option value="none">None</option> |
45 <option value="hist">History</option> | 49 <option value="hist">History</option> |
46 <option value="ref">Cached Reference</option> | 50 <option value="ref">Cached Reference</option> |
47 </param> | 51 </param> |
48 <when value="none"/> | 52 <when value="none"/> |
49 <when value="ref"> | 53 <when value="ref"> |
50 <param name="taxonomy" type="select" format="taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"> | 54 <param name="taxonomy" type="select" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"> |
51 <options from_file="mothur_taxonomy.loc"> | 55 <options from_file="mothur_taxonomy.loc"> |
52 <column name="name" index="0" /> | 56 <column name="name" index="0" /> |
53 <column name="value" index="1" /> | 57 <column name="value" index="1" /> |
54 </options> | 58 </options> |
55 </param> | 59 </param> |
56 </when> | 60 </when> |
57 <when value="hist"> | 61 <when value="hist"> |
58 <param name="taxonomy" type="data" format="taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/> | 62 <param name="taxonomy" type="data" format="seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/> |
59 </when> | 63 </when> |
60 </conditional> | 64 </conditional> |
61 <param name="label" type="select" label="label - OTU Labels" multiple="true"> | 65 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
62 <options from_dataset="otu"> | 66 <options from_dataset="otu"> |
63 <column name="name" index="0"/> | 67 <column name="name" index="0"/> |
66 </param> | 70 </param> |
67 <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100"> | 71 <param name="cutoff" type="integer" value="60" label="cutoff - Confindence percentage cutoff between 1 and 100"> |
68 <validator type="in_range" message="Confindence percentage cutoff must be between 0 and 100" min="0" max="100"/> | 72 <validator type="in_range" message="Confindence percentage cutoff must be between 0 and 100" min="0" max="100"/> |
69 </param> | 73 </param> |
70 <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/> | 74 <param name="probs" type="boolean" falsevalue="--probs=false" truevalue="" checked="true" label="probs - Show probabilities"/> |
75 <param name="basis" type="select" label="basis - Summary file gives numbers of" help=""> | |
76 <option value="otu">OTU</option> | |
77 <option value="sequence">sequence</option> | |
78 </param> | |
79 <param name="group" type="data" format="groups" optional="true" label="group - Groups for summary file"/> | |
71 </inputs> | 80 </inputs> |
72 <outputs> | 81 <outputs> |
73 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 82 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
74 </outputs> | 83 </outputs> |
75 <requirements> | 84 <requirements> |
88 | 97 |
89 **Command Documenation** | 98 **Command Documenation** |
90 | 99 |
91 The classify.otu_ command assigns sequences to chosen taxonomy outline. | 100 The classify.otu_ command assigns sequences to chosen taxonomy outline. |
92 | 101 |
102 The basis parameter allows you indicate what you want the summary file to represent, options are otu and sequence. Default is otu. For example consider the following basis=sequence could give Clostridiales 3 105 16 43 46, where 105 is the total number of sequences whose otu classified to Clostridiales. 16 is the number of sequences in the otus from groupA, 43 is the number of sequences in the otus from groupB, and 46 is the number of sequences in the otus from groupC. Now for basis=otu could give Clostridiales 3 7 6 1 2, where 7 is the number of otus that classified to Clostridiales. 6 is the number of otus containing sequences from groupA, 1 is the number of otus containing sequences from groupB, and 2 is the number of otus containing sequences from groupC. | |
103 | |
93 .. _classify.otu: http://www.mothur.org/wiki/Classify.otu | 104 .. _classify.otu: http://www.mothur.org/wiki/Classify.otu |
94 | 105 |
95 | 106 |
96 </help> | 107 </help> |
97 </tool> | 108 </tool> |