Mercurial > repos > iuc > mothur_heatmap_bin

comparison heatmap.bin.xml @ 0:b0718c06e329 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:56:10 -0400
parents
children ac2fa6a167ad
comparison
equal deleted inserted replaced
-1:000000000000 0:b0718c06e329
1 <tool profile="16.07" id="mothur_heatmap_bin" name="Heatmap.bin" version="@WRAPPER_VERSION@.0">
2 <description>Generate a heatmap for OTUs</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$input.otu" input_otu.dat &&
14
15 echo 'heatmap.bin(
16 #if $input.otu.is_of_type("mothur.rabund"):
17 rabund=input_otu.dat,
18 #elif $input.otu.is_of_type("mothur.sabund"):
19 sabund=input_otu.dat,
20 #elif $input.otu.is_of_type("mothur.list"):
21 list=input_otu.dat,
22 #elif $input.otu.is_of_type("mothur.relabund"):
23 relabund=input_otu.dat,
24 #elif $input.otu.is_of_type("mothur.shared"):
25 shared=input_otu.dat,
26 #end if
27 #if $input.has_groups == 'yes' and $input.groups:
28 groups=${ str($input.groups).replace(",","-") },
29 #end if
30 #if $input.label:
31 label=${ str($input.label).replace(",","-") },
32 #end if
33 scale=$scale,
34 sorted=$sorted,
35 numotu=$numotu,
36 fontsize=$fontsize
37 )'
38 | sed 's/ //g' ## mothur trips over whitespace
39 | mothur
40 | tee mothur.out.log
41 ]]></command>
42 <inputs>
43 <conditional name="input">
44 <param name="has_groups" type="select" label="Generate Heatmap for">
45 <option value="no">list, rabund, sabund</option>
46 <option value="yes">shared, relabund</option>
47 </param>
48 <when value="no">
49 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund" label="list,rabund,sabund - OTU List"/>
50 <param name="label" type="select" label="label - OTU Labels" multiple="true">
51 <expand macro="labeloptions"/>
52 </param>
53 </when>
54 <when value="yes">
55 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund file - OTU List"/>
56 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
57 <options>
58 <filter type="data_meta" ref="otu" key="groups"/>
59 </options>
60 </param>
61 <param name="label" type="select" multiple="true" label="label - OTU Labels">
62 <expand macro="labeloptions"/>
63 </param>
64 </when>
65 </conditional>
66 <param name="scale" type="select" label="scale - Scaling for heatmap">
67 <option value="log10" selected="true">Log10</option>
68 <option value="log2">Log2</option>
69 <option value="linear">Linear</option>
70 </param>
71 <param name="sorted" type="select" label="sorted - Sort heatmap">
72 <option value="shared" selected="true">By shared</option>
73 <option value="none">Don't sort</option>
74 <option value="topotu">By Total OTUs</option>
75 <option value="topgroup">By Total Groups</option>
76 </param>
77 <param name="numotu" type="integer" value="0" min="0" label="numotu - Limit the number of OTUs displayed (ignored if 0)"/>
78 <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
79 </inputs>
80 <outputs>
81 <expand macro="logfile-output"/>
82 <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps">
83 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.bin\.svg"/>
84 </collection>
85 </outputs>
86 <tests>
87 <test>
88 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
89 <param name="has_groups" value="no"/>
90 <output_collection name="heatmaps" count="36">
91 <element name="0.26.heatmap" md5="8f0d5cb95808115e50729e6df60629cc"/>
92 </output_collection>
93 <expand macro="logfile-test"/>
94 </test>
95 <test>
96 <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
97 <param name="has_groups" value="yes"/>
98 <param name="groups" value="forest"/>
99 <param name="label" value="0.26"/>
100 <output_collection name="heatmaps" count="1">
101 <element name="0.26.heatmap" md5="b2b46b7e55f55e2b260cd6dc6ccb4485"/>
102 </output_collection>
103 <expand macro="logfile-test"/>
104 </test>
105 <test>
106 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
107 <param name="has_groups" value="yes"/>
108 <param name="label" value="0.03,0.26,0.55"/>
109 <param name="groups" value="forest,pasture"/>
110 <param name="fontsize" value="100"/>
111 <param name="scale" value="linear"/>
112 <param name="sorted" value="none"/>
113 <output_collection name="heatmaps" count="3">
114 <element name="0.26.heatmap" md5="b46ed47e441a30588f60e1554ff703bb"/>
115 </output_collection>
116 <expand macro="logfile-test"/>
117 </test>
118 </tests>
119 <help>
120 <![CDATA[
121
122 @MOTHUR_OVERVIEW@
123
124
125 **Command Documentation**
126
127 The heatmap.bin_ command generates a heat map from data provided in either a list_ or a shared_ file.
128
129 .. _list: https://www.mothur.org/wiki/List_file
130 .. _shared: https://www.mothur.org/wiki/Shared_file
131 .. _heatmap.bin: https://www.mothur.org/wiki/Heatmap.bin
132
133 v.1.21.0: Updated to Mothur 1.33
134 ]]>
135 </help>
136 <expand macro="citations"/>
137 </tool>