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comparison mothur/tools/mothur/get.relabund.xml @ 2:e990ac8a0f58

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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author jjohnson
date Tue, 07 Jun 2011 17:39:06 -0400
parents fcc0778f6987
children 7bfe1f843858
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1:fcc0778f6987 2:e990ac8a0f58
1 <tool id="mothur_get_relabund" name="Get.relabund" version="1.16.0"> 1 <tool id="mothur_get_relabund" name="Get.relabund" version="1.19.0">
2 <description>Calculate the relative abundance of each otu</description> 2 <description>Calculate the relative abundance of each otu</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='get.relabund' 5 --cmd='get.relabund'
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.relabund$:'$relabund 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.relabund$:'$relabund
7 --outputdir='$logfile.extra_files_path' 7 --outputdir='$logfile.extra_files_path'
8 --READ_cmd='read.otu' 8 --shared=$otu
9 #if $input.source == 'similarity': 9 #if $label.__str__ != "None" and len($label.__str__) > 0:
10 --READ_list=$input.otu 10 --label='$label'
11 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
12 --READ_group='$otu_group'
13 #end if
14 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
15 --READ_label='$input.label'
16 #end if
17 #elif $input.source == 'shared':
18 --READ_shared=$input.otu
19 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
20 --READ_label='$input.label'
21 #end if
22 #end if 11 #end if
23 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: 12 #if $groups.__str__ != "None" and len($groups.__str__) > 0:
24 --groups=$input.groups 13 --groups=$groups
25 #end if 14 #end if
26 #if $scale.__str__ != "None" and len($scale.__str__) > 0: 15 #if $scale.__str__ != "None" and len($scale.__str__) > 0:
27 --scale=$scale 16 --scale=$scale
28 #end if 17 #end if
29 </command> 18 </command>
30 <inputs> 19 <inputs>
31 <conditional name="input"> 20 <param name="otu" type="data" format="shared" label="shared - OTU Shared"
32 <param name="source" type="select" label="Get Relative abundance for"> 21 help="Use Make.shared to create a shared file from a list and a group file"/>
33 <option value="similarity">OTU list</option> 22 <param name="label" type="select" label="label - OTU Labels" multiple="true">
34 <option value="shared">OTU Shared</option> 23 <options from_dataset="otu">
35 </param> 24 <column name="name" index="0"/>
36 <when value="similarity"> 25 <column name="value" index="0"/>
37 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> 26 <filter type="unique_value" name="unq_lbl" column="0" />
38 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> 27 </options>
39 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 28 </param>
40 <options from_dataset="otu"> 29 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
41 <column name="name" index="0"/> 30 <options from_dataset="otu">
42 <column name="value" index="0"/> 31 <column name="name" index="1"/>
43 </options> 32 <column name="value" index="1"/>
44 </param> 33 <filter type="unique_value" name="unq_grp" column="1" />
45 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> 34 </options>
46 <options from_dataset="otu_group"> 35 </param>
47 <column name="name" index="1"/>
48 <column name="value" index="1"/>
49 <filter type="unique_value" name="unq_grp" column="1" />
50 </options>
51 </param>
52 </when>
53 <when value="shared">
54 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
55 <param name="label" type="select" label="label - OTU Labels" multiple="true">
56 <options from_dataset="otu">
57 <column name="name" index="0"/>
58 <column name="value" index="0"/>
59 <filter type="unique_value" name="unq_lbl" column="0" />
60 </options>
61 </param>
62 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
63 <options from_dataset="otu">
64 <column name="name" index="1"/>
65 <column name="value" index="1"/>
66 <filter type="unique_value" name="unq_grp" column="1" />
67 </options>
68 </param>
69 </when>
70 </conditional>
71 <param name="scale" type="select" label="scale - Scale by"> 36 <param name="scale" type="select" label="scale - Scale by">
72 <option value="">Use default</option> 37 <option value="">Use default</option>
73 <option value="totalgroup">Total Groups</option> 38 <option value="totalgroup" selected="true">Total Groups</option>
74 <option value="totalotu">Total OTUs</option> 39 <option value="totalotu">Total OTUs</option>
75 <option value="averagegroup">Average Groups</option> 40 <option value="averagegroup">Average Groups</option>
76 <option value="averageotu">Average OTUs</option> 41 <option value="averageotu">Average OTUs</option>
77 </param> 42 </param>
78 </inputs> 43 </inputs>
94 59
95 .. _Mothur: http://www.mothur.org/wiki/Main_Page 60 .. _Mothur: http://www.mothur.org/wiki/Main_Page
96 61
97 **Command Documenation** 62 **Command Documenation**
98 63
99 The get.relabund_ command calculates the relative abundance of each otu in a sample. It outputs a .relabund file. 64 The get.relabund_ command calculates the relative abundance of each otu in a sample from a shared_ file. It outputs a .relabund_ file.
100 65
66 .. _shared: http://www.mothur.org/wiki/Shared_file
101 .. _get.relabund: http://www.mothur.org/wiki/Get.relabund 67 .. _get.relabund: http://www.mothur.org/wiki/Get.relabund
102 68
103 </help> 69 </help>
104 </tool> 70 </tool>