Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/remove.groups.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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-1:000000000000 | 0:3202a38e44d9 |
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1 <tool id="mothur_remove_groups" name="Remove.groups" version="1.15.0"> | |
2 <description>Remove groups</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 #import re, os.path | |
6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] | |
7 ## adds .pick before the last extension to the input file | |
8 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] | |
9 --cmd='remove.groups' | |
10 --outputdir='$logfile.extra_files_path' | |
11 --group=$group_in | |
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 #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: | |
19 --fasta=$fasta_in | |
20 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] | |
21 #end if | |
22 #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: | |
23 --name=$name_in | |
24 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] | |
25 #end if | |
26 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: | |
27 --list=$list_in | |
28 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] | |
29 #end if | |
30 #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: | |
31 --taxonomy=$taxonomy_in | |
32 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] | |
33 #end if | |
34 --result=#echo ','.join($results) | |
35 | |
36 </command> | |
37 <inputs> | |
38 <param name="group_in" type="data" format="groups" label="group - Groups"/> | |
39 <param name="groups" type="select" optional="true" label="groups - Pick groups to remove" multiple="true"> | |
40 <options from_dataset="group_in"> | |
41 <column name="name" index="1"/> | |
42 <column name="value" index="1"/> | |
43 <filter type="unique_value" name="unq_grp" column="1" /> | |
44 </options> | |
45 </param> | |
46 <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Accession Names"/> | |
47 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> | |
48 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> | |
49 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> | |
50 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy"/> | |
51 </inputs> | |
52 <outputs> | |
53 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
54 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> | |
55 <!-- fix format --> | |
56 <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> | |
57 <filter>fasta_in != None</filter> | |
58 </data> | |
59 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name"> | |
60 <filter>name_in != None</filter> | |
61 </data> | |
62 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> | |
63 <filter>list_in != None</filter> | |
64 </data> | |
65 <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> | |
66 <filter>taxonomy_in != None</filter> | |
67 </data> | |
68 </outputs> | |
69 <requirements> | |
70 <requirement type="binary">mothur</requirement> | |
71 </requirements> | |
72 <tests> | |
73 </tests> | |
74 <help> | |
75 **Mothur Overview** | |
76 | |
77 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
78 in the Department of Microbiology and Immunology at The University of Michigan, | |
79 provides bioinformatics for the microbial ecology community. | |
80 | |
81 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
82 | |
83 **Command Documenation** | |
84 | |
85 The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy. | |
86 | |
87 .. _remove.groups: http://www.mothur.org/wiki/Remove.groups | |
88 | |
89 | |
90 </help> | |
91 </tool> |