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comparison mothur/tools/mothur/heatmap.sim.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_heatmap_sim" name="Heatmap.sim" version="1.16.0" force_history_refresh="True"> 1 <tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.19.0" force_history_refresh="True">
2 <description>Generate a heatmap for pariwise similarity</description> 2 <description>Generate a heatmap for pariwise similarity</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='heatmap.sim' 5 --cmd='heatmap.sim'
6 --result='^mothur.\S+\.logfile$:'$logfile
7 --outputdir='$logfile.extra_files_path' 6 --outputdir='$logfile.extra_files_path'
8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' 7 #if $as_datasets.__str__ == "yes":
9 --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg' 8 #if $input.source == 'shared':
10 #if $input.source == 'similarity': 9 --result='^mothur.\S+\.logfile$:'$logfile
11 --READ_cmd='read.otu' 10 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
12 --READ_list=$input.otu 11 --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg'
13 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: 12 #else:
14 --READ_group='$otu_group' 13 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.heatmap\.sim\.svg$:'$heatmap
15 #end if 14 #end if
16 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: 15 #else:
17 --label='$input.label' 16 --result='^mothur.\S+\.logfile$:'$logfile
18 #end if 17 #end if
19 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: 18 #if $input.source == 'shared':
20 --groups=$input.groups 19 --shared=$input.otu
21 #end if
22 #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
23 --calc='$input.calc'
24 #end if
25 #elif $input.source == 'shared':
26 --READ_cmd='read.otu'
27 --READ_shared=$input.otu
28 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: 20 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
29 --label='$input.label' 21 --label='$input.label'
30 #end if 22 #end if
31 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: 23 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
32 --groups=$input.groups 24 --groups=$input.groups
37 #elif $input.source == 'column': 29 #elif $input.source == 'column':
38 --column=$input.dist 30 --column=$input.dist
39 --name=$input.name 31 --name=$input.name
40 #elif $input.source == 'phylip': 32 #elif $input.source == 'phylip':
41 --phylip=$input.dist 33 --phylip=$input.dist
42 #if $input.name.__str__ != "None" and len($input.name.__str__) > 0:
43 --name=$input.name
44 #end if
45 #end if 34 #end if
46 </command> 35 </command>
47 <inputs> 36 <inputs>
48 <!-- get.relabund relabund type should also work -->
49 <conditional name="input"> 37 <conditional name="input">
50 <param name="source" type="select" label="Generate Heatmap for"> 38 <param name="source" type="select" label="Generate Heatmap for">
51 <option value="similarity">OTU list</option> 39 <option value="shared">shared - Sample Similarity - OTU Shared</option>
52 <option value="shared">OTU Shared</option> 40 <option value="phylip">phylip - Phylip Distance Matrix</option>
53 <option value="column">Pairwise Column Distance Matrix</option> 41 <option value="column">colomn - Pairwise Column Distance Matrix</option>
54 <option value="phylip">Phylip Distance Matrix</option>
55 </param> 42 </param>
56 <when value="similarity">
57 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
58 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/>
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 </options>
64 </param>
65 <param name="groups" type="select" label="groups - Groups to include" multiple="true">
66 <options from_dataset="otu_group">
67 <column name="name" index="1"/>
68 <column name="value" index="1"/>
69 <filter type="unique_value" name="unq_grp" column="1" />
70 </options>
71 </param>
72 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
73 <options from_file="mothur_calculators.loc">
74 <column name="mult2" index="2"/>
75 <column name="name" index="0"/>
76 <column name="value" index="0"/>
77 <filter type="static_value" name="mult2" column="2" value="shar" />
78 </options>
79 </param>
80 </when>
81 <when value="shared"> 43 <when value="shared">
82 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> 44 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
83 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 45 <param name="label" type="select" label="label - OTU Labels" multiple="true">
84 <options from_dataset="otu"> 46 <options from_dataset="otu">
85 <column name="name" index="0"/> 47 <column name="name" index="0"/>
92 <column name="name" index="1"/> 54 <column name="name" index="1"/>
93 <column name="value" index="1"/> 55 <column name="value" index="1"/>
94 <filter type="unique_value" name="unq_grp" column="1" /> 56 <filter type="unique_value" name="unq_grp" column="1" />
95 </options> 57 </options>
96 </param> 58 </param>
59 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
60 <options from_file="mothur_calculators.loc">
61 <column name="mult2" index="2"/>
62 <column name="name" index="0"/>
63 <column name="value" index="0"/>
64 <filter type="static_value" name="mult2" column="2" value="shar" />
65 </options>
66 </param>
97 </when> 67 </when>
98 <when value="column"> 68 <when value="column">
99 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> 69 <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
100 <param name="name" type="data" format="names" label="name - Names"/> 70 <param name="name" type="data" format="names" label="name - Names"/>
101 </when> 71 </when>
102 <when value="phylip"> 72 <when value="phylip">
103 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> 73 <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
104 <param name="name" type="data" format="names" optional="true" label="name - Names"/>
105 </when> 74 </when>
106 </conditional> 75 </conditional>
76 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
107 </inputs> 77 </inputs>
108 <outputs> 78 <outputs>
109 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> 79 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
80 <data format="svg" name="heatmap" label="${tool.name} on ${on_string}: heatmap.sim.svg">
81 <filter>as_datasets != 'true' and input['source'] != 'shared'</filter>
82 </data>
110 </outputs> 83 </outputs>
111 <requirements> 84 <requirements>
112 <requirement type="binary">mothur</requirement> 85 <requirement type="binary">mothur</requirement>
113 </requirements> 86 </requirements>
114 <tests> 87 <tests>
122 95
123 .. _Mothur: http://www.mothur.org/wiki/Main_Page 96 .. _Mothur: http://www.mothur.org/wiki/Main_Page
124 97
125 **Command Documenation** 98 **Command Documenation**
126 99
127 The heatmap.sim_ command generates a heat map from data provided in either a .list or a .shared file. 100 The heatmap.sim_ command generates a heat map from data provided in either a shared_ file, a phylip_ distance matrix, or a column_ distance matrix and a name_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators
128 101
102 .. _shared: http://www.mothur.org/wiki/Shared_file
103 .. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
104 .. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix
105 .. _name: http://www.mothur.org/wiki/Name_file
129 .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim 106 .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim
130 107
131 </help> 108 </help>
132 </tool> 109 </tool>