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comparison mothur/tools/mothur/rarefaction.shared.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
comparison
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1:fcc0778f6987 2:e990ac8a0f58
1 <tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.16.0"> 1 <tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.19.0">
2 <description>Generate inter-sample rarefaction curves for OTUs</description> 2 <description>Generate inter-sample rarefaction curves for OTUs</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='rarefaction.shared' 5 --cmd='rarefaction.shared'
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rarefaction$:'$rarefaction 6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rarefaction$:'$rarefaction
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 int($iters.__str__) > 0: 15 #if int($iters.__str__) > 0:
27 --iters=$iters 16 --iters=$iters
28 #end if 17 #end if
29 $jumble 18 $jumble
30 #if $calc.__str__ != "None" and len($calc.__str__) > 0: 19 #if $calc.__str__ != "None" and len($calc.__str__) > 0:
31 --calc='$calc' 20 --calc='$calc'
32 #end if 21 #end if
33 </command> 22 </command>
34 <inputs> 23 <inputs>
35 <conditional name="input"> 24 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
36 <param name="source" type="select" label="Generate Heatmap for"> 25 <param name="label" type="select" label="label - OTU Labels" multiple="true">
37 <option value="similarity">OTU list</option> 26 <options from_dataset="otu">
38 <option value="shared">OTU Shared</option> 27 <column name="name" index="0"/>
39 </param> 28 <column name="value" index="0"/>
40 <when value="similarity"> 29 <filter type="unique_value" name="unq_lbl" column="0" />
41 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> 30 </options>
42 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> 31 </param>
43 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 32 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
44 <options from_dataset="otu"> 33 <help>All groups will be analyzed by default if none are selected</help>
45 <column name="name" index="0"/> 34 <options from_dataset="otu">
46 <column name="value" index="0"/> 35 <column name="name" index="1"/>
47 </options> 36 <column name="value" index="1"/>
48 </param> 37 <filter type="unique_value" name="unq_grp" column="1" />
49 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> 38 <filter type="add_value" name="all" value="all" />
50 <options from_dataset="otu_group"> 39 </options>
51 <column name="name" index="1"/> 40 </param>
52 <column name="value" index="1"/>
53 <filter type="unique_value" name="unq_grp" column="1" />
54 </options>
55 </param>
56 </when>
57 <when value="shared">
58 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
59 <param name="label" type="select" label="label - OTU Labels" multiple="true">
60 <options from_dataset="otu">
61 <column name="name" index="0"/>
62 <column name="value" index="0"/>
63 <filter type="unique_value" name="unq_lbl" column="0" />
64 </options>
65 </param>
66 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
67 <options from_dataset="otu">
68 <column name="name" index="1"/>
69 <column name="value" index="1"/>
70 <filter type="unique_value" name="unq_grp" column="1" />
71 </options>
72 </param>
73 </when>
74 </conditional>
75 <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/> 41 <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/>
76 <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/> 42 <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/>
77 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> 43 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
78 <options from_file="mothur_calculators.loc"> 44 <options from_file="mothur_calculators.loc">
79 <column name="mult2" index="2"/> 45 <column name="mult2" index="2"/>
101 67
102 .. _Mothur: http://www.mothur.org/wiki/Main_Page 68 .. _Mothur: http://www.mothur.org/wiki/Main_Page
103 69
104 **Command Documenation** 70 **Command Documenation**
105 71
106 The rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual. 72 The rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual. For calc parameter choices see: http://www.mothur.org/wiki/Calculators
107 73
108 .. _rarefaction.shared: http://www.mothur.org/wiki/Rarefaction.shared 74 .. _rarefaction.shared: http://www.mothur.org/wiki/Rarefaction.shared
109 75
110 </help> 76 </help>
111 </tool> 77 </tool>