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comparison mothur/tools/mothur/venn.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_venn" name="Venn" version="1.16.0" force_history_refresh="True"> 1 <tool id="mothur_venn" name="Venn" version="1.19.0" force_history_refresh="True">
2 <description>Generate Venn diagrams gor groups </description> 2 <description>Generate Venn diagrams for groups </description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='venn' 5 --cmd='venn'
6 --result='^mothur.\S+\.logfile$:'$logfile 6 --result='^mothur.\S+\.logfile$:'$logfile
7 --outputdir='$logfile.extra_files_path' 7 --outputdir='$logfile.extra_files_path'
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 8 #if $as_datasets.__str__ == "yes":
9 --new_datasets='^\S+?\.(\S+\.svg)$:svg' 9 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
10 --READ_cmd='read.otu' 10 --new_datasets='^\S+?\.(\S+\.svg)$:svg'
11 #if $input.source == 'similarity': 11 #end if
12 --READ_list=$input.otu 12 #if $input.source == 'shared':
13 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: 13 --shared=$input.otu
14 --READ_group='$otu_group'
15 #end if
16 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: 14 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
17 --label='$input.label' 15 --label='$input.label'
18 #end if 16 #end if
19 #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0: 17 #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
20 --calc='$input.calc' 18 --calc='$input.calc'
21 #end if 19 #end if
22 #elif $input.source == 'shared': 20 $nseqs
23 --READ_shared=$input.otu 21 $permute
22 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
23 --groups=$input.groups
24 #end if
25 #elif $input.source == 'similarity':
26 --list=$input.otu
24 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: 27 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
25 --label='$input.label' 28 --label='$input.label'
26 #end if 29 #end if
27 #if $calc.__str__ != "None" and len($calc.__str__) > 0: 30 #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
28 --calc='$calc' 31 --calc='$input.calc'
29 #end if 32 #end if
30 $nseqs 33 #if $input.abund >= 5:
31 $permute 34 --abund='$input.abund'
32 #end if 35 #end if
33 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: 36
34 --groups=$input.groups
35 #end if 37 #end if
36 </command> 38 </command>
37 <inputs> 39 <inputs>
38 <!-- get.relabund relabund type should also work -->
39 <conditional name="input"> 40 <conditional name="input">
40 <param name="source" type="select" label="Generate Heatmap for"> 41 <param name="source" type="select" label="Generate Heatmap for">
42 <option value="shared">OTU Shared</option>
41 <option value="similarity">OTU list</option> 43 <option value="similarity">OTU list</option>
42 <option value="shared">OTU Shared</option>
43 </param> 44 </param>
44 <when value="similarity"> 45 <when value="shared">
45 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> 46 <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
46 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/>
47 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)"> 47 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
48 <option value="sob">Chao</option> 48 <option value="sharedsobs">Shared Sobs</option>
49 <option value="chao">Chao</option>
50 <option value="ace">Ace</option>
51 </param>
52 <param name="label" type="select" label="label - OTU Labels" multiple="true">
53 <options from_dataset="otu">
54 <column name="name" index="0"/>
55 <column name="value" index="0"/>
56 </options>
57 </param>
58 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
59 <options from_dataset="otu_group">
60 <column name="name" index="1"/>
61 <column name="value" index="1"/>
62 <filter type="unique_value" name="unq_grp" column="1" />
63 </options>
64 </param>
65 </when>
66 <when value="shared">
67 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
68 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
69 <option value="sharedsobs">Shared Chao</option>
70 <option value="sharedchao">Shared Chao</option> 49 <option value="sharedchao">Shared Chao</option>
71 <option value="sharedace">Shared Ace</option> 50 <option value="sharedace">Shared Ace</option>
72 </param> 51 </param>
73 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 52 <param name="label" type="select" label="label - OTU Labels" multiple="true">
74 <options from_dataset="otu"> 53 <options from_dataset="otu">
83 <column name="value" index="1"/> 62 <column name="value" index="1"/>
84 <filter type="unique_value" name="unq_grp" column="1" /> 63 <filter type="unique_value" name="unq_grp" column="1" />
85 </options> 64 </options>
86 </param> 65 </param>
87 </when> 66 </when>
67 <when value="similarity">
68 <param name="otu" type="data" format="list" label="list - OTU List"/>
69 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
70 <option value="sobs">Sobs</option>
71 <option value="chao">Chao</option>
72 <option value="ace">Ace</option>
73 </param>
74 <param name="abund" type="integer" value="10" label="abund - Abundance when using the ace calculator ( >= 5 )">
75 <validator type="in_range" min="5" />
76 </param>
77 <param name="label" type="select" label="label - OTU Labels" multiple="true">
78 <options from_dataset="otu">
79 <column name="name" index="0"/>
80 <column name="value" index="0"/>
81 </options>
82 </param>
83 </when>
88 </conditional> 84 </conditional>
89 <param name="nseqs" type="boolean" truevalue="--nseqs=true" falsevalue="" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/> 85 <param name="nseqs" type="boolean" truevalue="--nseqs=true" falsevalue="" checked="false" label="nseqs - Output the number of sequences represented by the otus in the picture"/>
90 <param name="permute" type="boolean" truevalue="--permute=true" falsevalue="" checked="false" label="permute - Create pictures with all possible 4-way permutations of groups"/> 86 <param name="permute" type="boolean" truevalue="--permute=true" falsevalue="" checked="false" label="permute - Create pictures with all possible 4-way permutations of groups"/>
87 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
91 </inputs> 88 </inputs>
92 <outputs> 89 <outputs>
93 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> 90 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
94 </outputs> 91 </outputs>
95 <requirements> 92 <requirements>
106 103
107 .. _Mothur: http://www.mothur.org/wiki/Main_Page 104 .. _Mothur: http://www.mothur.org/wiki/Main_Page
108 105
109 **Command Documenation** 106 **Command Documenation**
110 107
111 The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. 108 The venn_ command generates Venn diagrams to compare the richness shared among 2, 3, or 4 groups. For calc parameter choices see: http://www.mothur.org/wiki/Calculators
112 109
113 .. _venn: http://www.mothur.org/wiki/Venn 110 .. _venn: http://www.mothur.org/wiki/Venn
114 111
115 </help> 112 </help>
116 </tool> 113 </tool>