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comparison mothur/tools/mothur/get.sabund.xml @ 35:95d75b35e4d2

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Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author certain cat
date Fri, 31 Oct 2014 15:09:32 -0400
parents 49058b1f8d3f
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34:1be61ceb20d7 35:95d75b35e4d2
1 <tool id="mothur_get_sabund" name="Get.sabund" version="1.19.0"> 1 <tool id="mothur_get_sabund" name="Get.sabund" version="1.20.0">
2 <description>Get sabund from a otu list or rabund</description> 2 <description>Get sabund from a otu list or rabund</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='get.sabund' 5 --cmd='get.sabund'
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund
7 --outputdir='$logfile.extra_files_path' 7 --outputdir='$logfile.extra_files_path'
8 #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): 8 #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
9 --list=$otu 9 --list=$otu
10 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): 10 #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
11 --rabund=$otu 11 --rabund=$otu
12 #end if 12 #end if
13 #if $label.__str__ != "None" and len($label.__str__) > 0: 13 #if $label.__str__ != "None" and len($label.__str__) > 0:
14 --label=$label 14 --label=$label
15 #end if 15 #end if
16 </command> 16 #if $count.__str__ != "None" and len($count.__str__) > 0:
17 <inputs> 17 --count=$count
18 <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/> 18 #end if
19 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)"> 19 </command>
20 <options> 20 <inputs>
21 <filter type="data_meta" ref="otu" key="labels" /> 21 <param name="otu" type="data" format="list,rabund" label="list,rabund - List or Rabund"/>
22 </options> 22 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
23 </param> 23 <options>
24 </inputs> 24 <filter type="data_meta" ref="otu" key="labels" />
25 <outputs> 25 </options>
26 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> 26 </param>
27 <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> 27 <param name = "count" type="data" format="count_table" optional="true" help ="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/>
28 </outputs>
29 <requirements>
30 <requirement type="package" version="1.27">mothur</requirement>
31 </requirements>
32 <tests>
33 </tests>
34 <help>
35 **Mothur Overview**
36 28
37 Mothur_, initiated by Dr. Patrick Schloss and his software development team 29 </inputs>
38 in the Department of Microbiology and Immunology at The University of Michigan, 30 <outputs>
39 provides bioinformatics for the microbial ecology community. 31 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
32 <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
33 </outputs>
34 <requirements>
35 <requirement type="package" version="1.33">mothur</requirement>
36 </requirements>
37 <tests>
38 </tests>
39 <help>
40 **Mothur Overview**
40 41
41 .. _Mothur: http://www.mothur.org/wiki/Main_Page 42 Mothur_, initiated by Dr. Patrick Schloss and his software development team
43 in the Department of Microbiology and Immunology at The University of Michigan,
44 provides bioinformatics for the microbial ecology community.
42 45
43 **Command Documenation** 46 .. _Mothur: http://www.mothur.org/wiki/Main_Page
44 47
45 The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file. 48 **Command Documenation**
46 49
47 .. _sabund: http://www.mothur.org/wiki/Sabund_file 50 The get.sabund_ command generates an sabund_ file from a list_ or rabund_ file.
48 .. _list: http://www.mothur.org/wiki/List_file 51
49 .. _rabund: http://www.mothur.org/wiki/Rabund_file 52 .. _sabund: http://www.mothur.org/wiki/Sabund_file
50 .. _get.sabund: http://www.mothur.org/wiki/Get.sabund 53 .. _list: http://www.mothur.org/wiki/List_file
54 .. _rabund: http://www.mothur.org/wiki/Rabund_file
55 .. _get.sabund: http://www.mothur.org/wiki/Get.sabund
51 56
52 57
53 </help> 58 </help>
54 </tool> 59 </tool>