Mercurial > repos > iuc > mothur_heatmap_sim

comparison heatmap.sim.xml @ 0:edf78e2b71d4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:35:34 -0400
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-1:000000000000 0:edf78e2b71d4
1 <tool profile="16.07" id="mothur_heatmap_sim" name="Heatmap.sim" version="@WRAPPER_VERSION@.0">
2 <description>Generate a heatmap for pariwise similarity</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 ## create symlinks to input datasets
10 ln -s "$count" count.dat &&
11 #if $input.source == 'shared':
12 ln -s "$input.otu" input_otu.dat &&
13 #else
14 ln -s "$input.dist" input_dist.dat &&
15 #if $input.source == 'column':
16 ln -s "$input.name" input_name.dat &&
17 #end if
18 #end if
19
20 echo 'heatmap.sim(
21 #if $input.source == "shared":
22 shared=input_otu.dat,
23 #if $input.label:
24 label=${ str($input.label).replace(",","-") },
25 #end if
26 #if $input.groups:
27 groups=${ str($input.groups).replace(",","-") },
28 #end if
29 #if $input.calc:
30 calc=${ str($input.calc).replace(",","-") },
31 #end if
32 #elif $input.source == "column":
33 column=input_dist.dat,
34 name=input_name.dat,
35 #elif $input.source == "phylip":
36 phylip=input_dist.dat,
37 #end if
38 #if $count:
39 count=count.dat,
40 #end if
41 fontsize=$fontsize
42 )'
43 | sed 's/ //g' ## mothur trips over whitespace
44 | mothur
45 ]]></command>
46 <inputs>
47 <conditional name="input">
48 <param name="source" type="select" label="Generate Heatmap for">
49 <option value="shared">shared - Sample Similarity - OTU Shared</option>
50 <option value="phylip">phylip - Phylip Distance Matrix</option>
51 <option value="column">colomn - Pairwise Column Distance Matrix</option>
52 </param>
53 <when value="shared">
54 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
55 <param name="label" type="select" label="label - OTU Labels" multiple="true">
56 <expand macro="labeloptions"/>
57 </param>
58 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
59 <options>
60 <filter type="data_meta" ref="otu" key="groups"/>
61 </options>
62 </param>
63 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
64 <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
65 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
66 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
67 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
68 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
69 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
70 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
71 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
72 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
73 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
74 </param>
75 </when>
76 <when value="column">
77 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
78 <param name="name" type="data" format="mothur.names" label="name - Names"/>
79 </when>
80 <when value="phylip">
81 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
82 </when>
83 </conditional>
84 <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
85 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="generated by count.seqs"/>
86 </inputs>
87 <outputs>
88 <expand macro="logfile-output"/>
89 <data name="heatmap" format="svg" from_work_dir="input_dist*.heatmap.sim.svg" label="${tool.name} on ${on_string}: heatmap.sim.svg">
90 <filter>input['source'] != 'shared'</filter>
91 </data>
92 <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps">
93 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.sim\.svg"/>
94 <filter>input['source'] == 'shared'</filter>
95 </collection>
96 </outputs>
97 <tests>
98 <test>
99 <param name="source" value="phylip"/>
100 <param name="dist" value="amazon.dist" ftype="mothur.square.dist"/>
101 <output name="heatmap">
102 <assert_contents>
103 <has_text text="svg xmlns:svg="/>
104 <has_text text="Heatmap for"/>
105 <has_text text="U68640"/>
106 </assert_contents>
107 </output>
108 <expand macro="logfile-test"/>
109 </test>
110 <test>
111 <param name="source" value="shared"/>
112 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
113 <output_collection name="heatmaps" count="72">
114 <element name="0.55.jest.heatmap" md5="c48bac26a84f657ead8dd43af0401317"/>
115 </output_collection>
116 <expand macro="logfile-test"/>
117 </test>
118 <test>
119 <param name="source" value="shared"/>
120 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
121 <param name="label" value="0.03,0.26,0.55"/>
122 <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/>
123 <param name="groups" value="forest,pasture"/>
124 <output_collection name="heatmaps" count="30">
125 <element name="0.03.braycurtis.heatmap" md5="6a3f261e1012edaf620f78b62eff5c88"/>
126 </output_collection>
127 <expand macro="logfile-test"/>
128 </test>
129 </tests>
130 <help>
131 <![CDATA[
132
133 @MOTHUR_OVERVIEW@
134
135 **Command Documenation**
136
137 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
138
139 .. _shared: http://www.mothur.org/wiki/Shared_file
140 .. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
141 .. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix
142 .. _name: http://www.mothur.org/wiki/Name_file
143 .. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim
144
145 v.1.24.0: Updated to Mothur 1.33, added count parameter
146 ]]>
147 </help>
148 <expand macro="citations"/>
149 </tool>