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comparison mothur/tools/mothur/heatmap.bin.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_bin" name="Heatmap.bin" version="1.16.0" force_history_refresh="True"> 1 <tool id="mothur_heatmap_bin" name="Heatmap.bin" version="1.19.0" force_history_refresh="True">
2 <description>Generate a heatmap for OTUs</description> 2 <description>Generate a heatmap for OTUs</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 mothur_wrapper.py 4 mothur_wrapper.py
5 --cmd='heatmap.bin' 5 --cmd='heatmap.bin'
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 $as_datasets.__str__ == "yes":
9 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$:svg' 9 --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
10 --READ_cmd='read.otu' 10 --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.heatmap\.bin\.svg)$:svg'
11 #if $input.source == 'similarity':
12 --READ_list=$input.otu
13 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
14 --READ_group='$otu_group'
15 #end if
16 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
17 --READ_label='$input.label'
18 #end if
19 #elif $input.source == 'shared':
20 --READ_relabund=$input.otu
21 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
22 --READ_label='$input.label'
23 #end if
24 #end if 11 #end if
25 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: 12 #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
13 --shared=$input.otu
14 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
15 --rabund=$input.otu
16 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):
17 --sabund=$input.otu
18 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__):
19 --list=$input.otu
20 #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__):
21 --relabund=$input.otu
22 #end if
23 #if $input.has_groups != 'no' and $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
26 --groups=$input.groups 24 --groups=$input.groups
25 #end if
26 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
27 --label='$input.label'
27 #end if 28 #end if
28 #if $scale.__str__ != "None" and len($scale.__str__) > 0: 29 #if $scale.__str__ != "None" and len($scale.__str__) > 0:
29 --scale='$scale' 30 --scale='$scale'
30 #end if 31 #end if
31 #if $sorted.__str__ != "None" and len($sorted.__str__) > 0: 32 #if $sorted.__str__ != "None" and len($sorted.__str__) > 0:
37 #if 100 > $fontsize > 0: 38 #if 100 > $fontsize > 0:
38 --fontsize=$fontsize 39 --fontsize=$fontsize
39 #end if 40 #end if
40 </command> 41 </command>
41 <inputs> 42 <inputs>
42 <!-- get.relabund relabund type should also work --> 43 <conditional name="input">
43 <conditional name="input"> 44 <param name="has_groups" type="select" label="Generate Heatmap for">
44 <param name="source" type="select" label="Generate Heatmap for"> 45 <option value="default">shared or relabund</option>
45 <option value="similarity">OTU list</option> 46 <option value="no">list, rabund, sabund</option>
46 <option value="relabund">OTU Relative Abundance</option> 47 <option value="yes">list, rabund, sabund with groups</option>
47 </param> 48 </param>
48 <when value="similarity"> 49 <when value="default">
49 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> 50 <param name="otu" type="data" format="shared,relabund" label="shared,relabund - OTU List"/>
50 <param name="otu_group" type="data" format="groups" label="read.otu(group) - Group file for the OTU List"/> 51 <param name="groups" type="select" label="groups - Groups to condider" multiple="true">
52 <options from_dataset="otu">
53 <column name="name" index="1"/>
54 <column name="value" index="1"/>
55 <filter type="unique_value" name="unq_grp" column="1" />
56 </options>
57 </param>
51 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 58 <param name="label" type="select" label="label - OTU Labels" multiple="true">
52 <options from_dataset="otu"> 59 <options from_dataset="otu">
53 <column name="name" index="0"/> 60 <column name="name" index="0"/>
54 <column name="value" index="0"/> 61 <column name="value" index="0"/>
62 <filter type="unique_value" name="unq_lbl" column="0" />
55 </options> 63 </options>
56 </param> 64 </param>
57 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> 65 </when>
66 <when value="no">
67 <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/>
68 <param name="label" type="select" label="label - OTU Labels" multiple="true">
69 <options from_dataset="otu">
70 <column name="name" index="0"/>
71 <column name="value" index="0"/>
72 <filter type="unique_value" name="unq_lbl" column="0" />
73 </options>
74 </param>
75 </when>
76 <when value="yes">
77 <param name="otu" type="data" format="list,rabund,sabund" label="list,rabund,sabund - OTU List"/>
78 <param name="otu_group" type="data" format="groups" label="read.otu(group) - Group file for the OTU List"/>
79 <param name="groups" type="select" label="groups - Groups to include" multiple="true">
58 <options from_dataset="otu_group"> 80 <options from_dataset="otu_group">
59 <column name="name" index="1"/> 81 <column name="name" index="1"/>
60 <column name="value" index="1"/> 82 <column name="value" index="1"/>
61 <filter type="unique_value" name="unq_grp" column="1" /> 83 <filter type="unique_value" name="unq_grp" column="1" />
62 </options> 84 </options>
63 </param> 85 </param>
64 </when>
65 <when value="relabund">
66 <param name="otu" type="data" format="relabund" label="read.otu(relabund=) - OTU Relative Abundance"/>
67 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 86 <param name="label" type="select" label="label - OTU Labels" multiple="true">
68 <options from_dataset="otu"> 87 <options from_dataset="otu">
69 <column name="name" index="0"/> 88 <column name="name" index="0"/>
70 <column name="value" index="0"/> 89 <column name="value" index="0"/>
71 </options> 90 <filter type="unique_value" name="unq_lbl" column="0" />
72 </param>
73 <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
74 <options from_dataset="otu">
75 <column name="name" index="1"/>
76 <column name="value" index="1"/>
77 <filter type="unique_value" name="unq_grp" column="1" />
78 </options> 91 </options>
79 </param> 92 </param>
80 </when> 93 </when>
81 </conditional> 94 </conditional>
82 <param name="scale" type="select" label="scale - Scaling for heatmap"> 95 <param name="scale" type="select" label="scale - Scaling for heatmap">
86 <option value="linear">Linear</option> 99 <option value="linear">Linear</option>
87 </param> 100 </param>
88 <param name="sorted" type="select" label="sorted - Sort heatmap"> 101 <param name="sorted" type="select" label="sorted - Sort heatmap">
89 <option value="">By shared</option> 102 <option value="">By shared</option>
90 <option value="none">Don't sort</option> 103 <option value="none">Don't sort</option>
91 <option value="totalotu">By Total OTUs</option> 104 <option value="topotu">By Total OTUs</option>
92 <option value="totalgroup">By Total Groups</option> 105 <option value="topgroup">By Total Groups</option>
93 </param> 106 </param>
94 <param name="numotu" type="integer" value="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/> 107 <param name="numotu" type="integer" value="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/>
95 <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/> 108 <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
109 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
96 </inputs> 110 </inputs>
97 <outputs> 111 <outputs>
98 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> 112 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
99 </outputs> 113 </outputs>
100 <requirements> 114 <requirements>
111 125
112 .. _Mothur: http://www.mothur.org/wiki/Main_Page 126 .. _Mothur: http://www.mothur.org/wiki/Main_Page
113 127
114 **Command Documenation** 128 **Command Documenation**
115 129
116 The heatmap.bin_ command generates a heat map from data provided in either a .list or a .shared file. 130 The heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file.
117 131
132 .. _list: http://www.mothur.org/wiki/List_file
133 .. _shared: http://www.mothur.org/wiki/Shared_file
118 .. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin 134 .. _heatmap.bin: http://www.mothur.org/wiki/Heatmap.bin
119 135
120 </help> 136 </help>
121 </tool> 137 </tool>