Mercurial > repos > iuc > mothur_heatmap_sim

comparison heatmap.sim.xml @ 0:002aec843953 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:21:12 -0400
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children 6c7e2e05f606
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-1:000000000000 0:002aec843953
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="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
12 ## create symlinks to input datasets
13 ln -s "$count" count.dat &&
14 #if $input.source == 'shared':
15 ln -s "$input.otu" input_otu.dat &&
16 #else
17 ln -s "$input.dist" input_dist.dat &&
18 #if $input.source == 'column':
19 ln -s "$input.name" input_name.dat &&
20 #end if
21 #end if
22
23 echo 'heatmap.sim(
24 #if $input.source == "shared":
25 shared=input_otu.dat,
26 #if $input.label:
27 label=${ str($input.label).replace(",","-") },
28 #end if
29 #if $input.groups:
30 groups=${ str($input.groups).replace(",","-") },
31 #end if
32 #if $input.calc:
33 calc=${ str($input.calc).replace(",","-") },
34 #end if
35 #elif $input.source == "column":
36 column=input_dist.dat,
37 name=input_name.dat,
38 #elif $input.source == "phylip":
39 phylip=input_dist.dat,
40 #end if
41 #if $count:
42 count=count.dat,
43 #end if
44 fontsize=$fontsize
45 )'
46 | sed 's/ //g' ## mothur trips over whitespace
47 | mothur
48 | tee mothur.out.log
49 ]]></command>
50 <inputs>
51 <conditional name="input">
52 <param name="source" type="select" label="Generate Heatmap for">
53 <option value="shared">shared - Sample Similarity - OTU Shared</option>
54 <option value="phylip">phylip - Phylip Distance Matrix</option>
55 <option value="column">colomn - Pairwise Column Distance Matrix</option>
56 </param>
57 <when value="shared">
58 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
59 <param name="label" type="select" label="label - OTU Labels" multiple="true">
60 <expand macro="labeloptions"/>
61 </param>
62 <param name="groups" type="select" multiple="true" label="groups - Groups to include">
63 <options>
64 <filter type="data_meta" ref="otu" key="groups"/>
65 </options>
66 </param>
67 <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none selected)">
68 <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
69 <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
70 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
71 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
72 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
73 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
74 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
75 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
76 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
77 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
78 </param>
79 </when>
80 <when value="column">
81 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
82 <param name="name" type="data" format="mothur.names" label="name - Names"/>
83 </when>
84 <when value="phylip">
85 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
86 </when>
87 </conditional>
88 <param name="fontsize" type="integer" value="24" min="0" max="100" label="fontsize - Fontsize (default is 24)"/>
89 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table" help="generated by count.seqs"/>
90 </inputs>
91 <outputs>
92 <expand macro="logfile-output"/>
93 <data name="heatmap" format="svg" from_work_dir="input_dist*.heatmap.sim.svg" label="${tool.name} on ${on_string}: heatmap.sim.svg">
94 <filter>input['source'] != 'shared'</filter>
95 </data>
96 <collection name="heatmaps" type="list" label="${tool.name} on ${on_string}: Heatmaps">
97 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.sim\.svg"/>
98 <filter>input['source'] == 'shared'</filter>
99 </collection>
100 </outputs>
101 <tests>
102 <test>
103 <param name="source" value="phylip"/>
104 <param name="dist" value="amazon.dist" ftype="mothur.square.dist"/>
105 <output name="heatmap">
106 <assert_contents>
107 <has_text text="svg xmlns:svg="/>
108 <has_text text="Heatmap for"/>
109 <has_text text="U68640"/>
110 </assert_contents>
111 </output>
112 <expand macro="logfile-test"/>
113 </test>
114 <test>
115 <param name="source" value="shared"/>
116 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
117 <output_collection name="heatmaps" count="72">
118 <element name="0.55.jest.heatmap" md5="c48bac26a84f657ead8dd43af0401317"/>
119 </output_collection>
120 <expand macro="logfile-test"/>
121 </test>
122 <test>
123 <param name="source" value="shared"/>
124 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
125 <param name="label" value="0.03,0.26,0.55"/>
126 <param name="calc" value="jclass,jest,sorclass,sorest,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc"/>
127 <param name="groups" value="forest,pasture"/>
128 <output_collection name="heatmaps" count="30">
129 <element name="0.03.braycurtis.heatmap" md5="6a3f261e1012edaf620f78b62eff5c88"/>
130 </output_collection>
131 <expand macro="logfile-test"/>
132 </test>
133 </tests>
134 <help>
135 <![CDATA[
136
137 @MOTHUR_OVERVIEW@
138
139 **Command Documentation**
140
141 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: https://www.mothur.org/wiki/Calculators
142
143 .. _shared: https://www.mothur.org/wiki/Shared_file
144 .. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
145 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
146 .. _name: https://www.mothur.org/wiki/Name_file
147 .. _heatmap.sim: https://www.mothur.org/wiki/Heatmap.sim
148
149 v.1.24.0: Updated to Mothur 1.33, added count parameter
150 ]]>
151 </help>
152 <expand macro="citations"/>
153 </tool>