Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/remove.otus.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
parents | |
children | fcc0778f6987 |
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1 <tool id="mothur_remove_otus" name="Remove.otus" version="1.15.0"> | |
2 <description>Remove otus containing sequences from specified groups</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list | |
6 #import re, os.path | |
7 --cmd='remove.otus' | |
8 --outputdir='$logfile.extra_files_path' | |
9 --group=$group_in | |
10 --list=$list_in | |
11 --label=$label | |
12 #if $groups.__str__ != "None" and len($groups.__str__) > 0: | |
13 --groups=$groups | |
14 #end if | |
15 #if $accnos.__str__ != "None" and len($accnos.__str__) > 0: | |
16 --accnos=$accnos | |
17 #end if | |
18 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] | |
19 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.' + $label.__str__ + '.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] | |
20 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.'+ $label.__str__ + '.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] | |
21 --result=#echo ','.join($results) | |
22 </command> | |
23 <inputs> | |
24 <param name="group_in" type="data" format="groups" label="group - Groups"/> | |
25 <param name="list_in" type="data" format="list" label="list - OTU List"/> | |
26 <param name="label" type="select" label="label - OTU Labels" > | |
27 <options from_dataset="list_in"> | |
28 <column name="name" index="0"/> | |
29 <column name="value" index="0"/> | |
30 </options> | |
31 </param> | |
32 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> | |
33 <options from_dataset="group_in"> | |
34 <column name="name" index="1"/> | |
35 <column name="value" index="1"/> | |
36 <filter type="unique_value" name="unq_grp" column="1" /> | |
37 </options> | |
38 </param> | |
39 <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Group Names from your history"/> | |
40 </inputs> | |
41 <outputs> | |
42 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
43 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> | |
44 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"/> | |
45 </outputs> | |
46 <requirements> | |
47 <requirement type="binary">mothur</requirement> | |
48 </requirements> | |
49 <tests> | |
50 </tests> | |
51 <help> | |
52 **Mothur Overview** | |
53 | |
54 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
55 in the Department of Microbiology and Immunology at The University of Michigan, | |
56 provides bioinformatics for the microbial ecology community. | |
57 | |
58 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
59 | |
60 **Command Documenation** | |
61 | |
62 The remove.otus_ command removes otus containing sequences from a specific group or set of groups. | |
63 | |
64 .. _remove.otus: http://www.mothur.org/wiki/Remove.otus | |
65 | |
66 | |
67 </help> | |
68 </tool> |