Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/make.shared.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 | |
children | 11867a45a43d |
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1 <tool id="mothur_make_shared" name="Make.shared" version="1.19.0" force_history_refresh="True"> | |
2 <description>Make a shared file from a list and a group</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 #import re, os.path | |
6 --cmd='make.shared' | |
7 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared$:'$shared | |
8 --outputdir='$logfile.extra_files_path' | |
9 #if $as_datasets.__str__ == "yes": | |
10 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' | |
11 --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' | |
12 #end if | |
13 --list=$list | |
14 --group=$group | |
15 #if $label.__str__ != "None" and len($label.__str__) > 0: | |
16 --label='$label' | |
17 #end if | |
18 #if $groups.__str__ != "None" and len($groups.__str__) > 0: | |
19 --unique=$groups | |
20 #end if | |
21 #if $ordergroup.__str__ != "None" and len($ordergroup.__str__) > 0: | |
22 --ordergroup=$ordergroup | |
23 #end if | |
24 </command> | |
25 <inputs> | |
26 <param name="list" type="data" format="list" label="list - OTU List"/> | |
27 <param name="group" type="data" format="groups" label="group - "/> | |
28 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" | |
29 help="By default all are included if no selection is made."> | |
30 <options from_dataset="list"> | |
31 <column name="name" index="0"/> | |
32 <column name="value" index="0"/> | |
33 </options> | |
34 </param> | |
35 <param name="groups" type="select" label="groups - Groups to include" multiple="true"> | |
36 <options from_dataset="group"> | |
37 <column name="name" index="1"/> | |
38 <column name="value" index="1"/> | |
39 <filter type="unique_value" name="unq_grp" column="1" /> | |
40 </options> | |
41 </param> | |
42 <param name="ordergroup" type="data" format="groups" optional="true" label="ordergroup - one column list of group names in desired order"/> | |
43 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each group rabund"/> | |
44 </inputs> | |
45 <outputs> | |
46 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
47 <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> | |
48 </outputs> | |
49 <requirements> | |
50 <requirement type="binary">mothur</requirement> | |
51 </requirements> | |
52 <tests> | |
53 </tests> | |
54 <help> | |
55 **Mothur Overview** | |
56 | |
57 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
58 in the Department of Microbiology and Immunology at The University of Michigan, | |
59 provides bioinformatics for the microbial ecology community. | |
60 | |
61 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
62 | |
63 **Command Documenation** | |
64 | |
65 The make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group. | |
66 | |
67 | |
68 .. _list: http://www.mothur.org/wiki/List_file | |
69 .. _group: http://www.mothur.org/wiki/Group_file | |
70 .. _shared: http://www.mothur.org/wiki/Shared_file | |
71 .. _rabund: http://www.mothur.org/wiki/Rabund_file | |
72 .. _make.shared: http://www.mothur.org/wiki/Make.shared | |
73 | |
74 </help> | |
75 </tool> |