Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/split.groups.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 | 5265aa9067e0 |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_split_groups" name="Split.groups" version="1.16.0" force_history_refresh="True"> | 1 <tool id="mothur_split_groups" name="Split.groups" version="1.19.0" force_history_refresh="True"> |
2 <description>Generates a fasta file for each group</description> | 2 <description>Generates a fasta file for each group</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 --cmd='split.groups' | 5 --cmd='split.groups' |
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+?\.(\S+\.fasta)$:fasta' | 9 --new_datasets='^\S+?\.(\S+\.fasta)$:fasta','^\S+?\.(\S+\.names)$:names' |
10 --fasta=$fasta | 10 --fasta=$fasta |
11 --group=$group | 11 --group=$group |
12 #if $name.__str__ != "None" and len($name.__str__) > 0: | |
13 --name=$name | |
14 #end if | |
15 #if $groups.__str__ != "None" and len($groups.__str__) > 0: | |
16 --groups=$groups | |
17 #end if | |
12 </command> | 18 </command> |
13 <inputs> | 19 <inputs> |
14 <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> | 20 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/> |
21 <param name="name" type="data" format="names" label="name - Names to split by group" optional="true"/> | |
15 <param name="group" type="data" format="groups" label="group - Groups"/> | 22 <param name="group" type="data" format="groups" label="group - Groups"/> |
23 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true"> | |
24 <options from_dataset="group"> | |
25 <column name="name" index="1"/> | |
26 <column name="value" index="1"/> | |
27 <filter type="unique_value" name="unq_grp" column="1" /> | |
28 </options> | |
29 </param> | |
16 </inputs> | 30 </inputs> |
17 <outputs> | 31 <outputs> |
18 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 32 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
19 </outputs> | 33 </outputs> |
20 <requirements> | 34 <requirements> |
31 | 45 |
32 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 46 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
33 | 47 |
34 **Command Documenation** | 48 **Command Documenation** |
35 | 49 |
36 The split.groups_ command reads a fasta file group file and generates a fasta file for each group in the groupfile. | 50 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups. |
37 | 51 |
52 .. _group: http://www.mothur.org/wiki/Group_file | |
53 .. _name: http://www.mothur.org/wiki/Name_file | |
38 .. _split.groups: http://www.mothur.org/wiki/Split.groups | 54 .. _split.groups: http://www.mothur.org/wiki/Split.groups |
39 | 55 |
40 </help> | 56 </help> |
41 </tool> | 57 </tool> |