Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/classify.tree.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
---|---|
date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
children |
rev | line source |
---|---|
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
1 <tool id="mothur_classify_tree" name="Classify.tree" version="1.25.0"> |
24
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
2 <description>Get a consensus taxonomy for each node on a tree</description> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
3 <command interpreter="python"> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
4 mothur_wrapper.py |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
5 --cmd='classify.tree' |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.taxonomy\.tre$:'$out_tree,'^\S+\.taxonomy\.summary$:'$summary |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
7 --outputdir='$logfile.extra_files_path' |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
8 --taxonomy=$taxonomy |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
9 --tree=$tree |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
10 #if $name.__str__ != "None" and len($name.__str__) > 0: |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
11 --name='$name' |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
12 #end if |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
13 #if $group.__str__ != "None" and len($group.__str__) > 0: |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
14 --group=$group |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
15 #end if |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
16 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
17 --name=$names |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
18 </command> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
19 <inputs> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
20 <param name="taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
21 <param name="tree" type="data" format="tre" label="tree - Sequences to filter"/> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
22 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference file"/> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
23 <param name="group" type="data" format="group" optional="true" label="group - Sequences Group reference"/> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
24 <param name="cutoff" type="integer" value="51" optional="true" label="cutoff - consensus confidence threshold" |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
25 help="The default is 51, meaning 51%. Cutoff cannot be below 51"> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
26 <validator type="in_range" message="The percentage cutoff must be between 51 and 100" min="51" max="100"/> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
27 </param> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
28 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
29 </inputs> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
30 <outputs> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
31 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
32 <data format_source="tree" name="out_tree" label="${tool.name} on ${on_string}: taxonomy.tre" /> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
33 <data format_source="tabular" name="summary" label="${tool.name} on ${on_string}: taxonomy.summary" /> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
34 </outputs> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
35 <requirements> |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
36 <requirement type="package" version="1.33">mothur</requirement> |
24
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
37 </requirements> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
38 <tests> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
39 </tests> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
40 <help> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
41 **Mothur Overview** |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
42 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
43 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
44 in the Department of Microbiology and Immunology at The University of Michigan, |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
45 provides bioinformatics for the microbial ecology community. |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
46 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
47 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
48 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
49 **Command Documenation** |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
50 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
51 The classify.tree_ command is used to get a consensus taxonomy for each node on a tree. |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
52 Input is a taxonomy_ and a tree_ with optional name_ or group_ reference. |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
53 The output is a tree_ and a summary.. |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
54 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
55 TreeNode NumRep Taxonomy |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
56 243 2 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100); |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
57 244 3 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100); |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
58 245 4 Bacteria(100);"Firmicutes"(100);"Clostridia"(100);Clostridiales(100);"Ruminococcaceae"(100);Faecalibacterium(100); |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
59 ... |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
60 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
61 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
62 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
63 .. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
64 .. _name: http://www.mothur.org/wiki/Name_file |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
65 .. _group: http://www.mothur.org/wiki/Group_file |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
66 .. _classify.tree: http://www.mothur.org/wiki/Classify.tree |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
67 |
35
95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
certain cat
parents:
27
diff
changeset
|
68 v.1.25.0: Trivial upgrade to Mothur 1.33 |
24
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
69 |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
70 </help> |
09740be2bc9c
Mothur - updates for Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents:
diff
changeset
|
71 </tool> |