Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/get.sabund.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 |
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children | bfbaf823be4c |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_get_sabund" name="Get.sabund" version="1.19.0"> | |
2 <description>Get sabund from a otu list or rabund</description> | |
3 <command interpreter="python"> | |
4 mothur_wrapper.py | |
5 --cmd='get.sabund' | |
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund | |
7 --outputdir='$logfile.extra_files_path' | |
8 #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): | |
9 --list=$otu | |
10 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): | |
11 --rabund=$otu | |
12 #end if | |
13 #if $label.__str__ != "None" and len($label.__str__) > 0: | |
14 --label=$label | |
15 #end if | |
16 </command> | |
17 <inputs> | |
18 <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/> | |
19 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> | |
20 <options from_dataset="otu"> | |
21 <column name="name" index="0"/> | |
22 <column name="value" index="0"/> | |
23 </options> | |
24 </param> | |
25 </inputs> | |
26 <outputs> | |
27 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | |
28 <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> | |
29 </outputs> | |
30 <requirements> | |
31 <requirement type="binary">mothur</requirement> | |
32 </requirements> | |
33 <tests> | |
34 </tests> | |
35 <help> | |
36 **Mothur Overview** | |
37 | |
38 Mothur_, initiated by Dr. Patrick Schloss and his software development team | |
39 in the Department of Microbiology and Immunology at The University of Michigan, | |
40 provides bioinformatics for the microbial ecology community. | |
41 | |
42 .. _Mothur: http://www.mothur.org/wiki/Main_Page | |
43 | |
44 **Command Documenation** | |
45 | |
46 The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file. | |
47 | |
48 .. _sabund: http://www.mothur.org/wiki/Sabund_file | |
49 .. _list: http://www.mothur.org/wiki/List_file | |
50 .. _rabund: http://www.mothur.org/wiki/Rabund_file | |
51 .. _get.sabund: http://www.mothur.org/wiki/Get.sabund | |
52 | |
53 | |
54 </help> | |
55 </tool> |