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author proteore
date Tue, 18 Dec 2018 09:58:49 -0500
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1 <tool id="heatmap" name="HeatMap" version="2018.12.12">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="4.7.1">r-plotly</requirement>
5 <requirement type="package" version="0.14.1">r-heatmaply</requirement>
6 <requirement type="package" version="2.1.1">phantomjs</requirement>
7 <requirement type="package" version="2.2.1">pandoc</requirement>
8 </requirements>
9 <command detect_errors="exit_code"><![CDATA[
10 Rscript $__tool_directory__/heatmap_viz.R
11 --input='$file'
12 --output="$file.name"
13 --type='$output_type'
14 --cols='$select_data_columns.cols'
15 --row_names=$rownames
16 --header='$header'
17 --col_text_angle='$angle_col'
18 --dist="$distance"
19 --clust="$clustering"
20 --dendrogram="$dendrogram"
21
22 ]]></command>
23 <inputs>
24 <param name="file" type="data" format="txt,tabular" label="Select your file (table)" help="" />
25 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file contain a header?" />
26 <conditional name="select_data_columns">
27 <param name="enter_cols" type="select" label="Select columns or a range of columns containing expression values">
28 <option value="cols_number">Select columns to be used one by one</option>
29 <option value="cols_range">Select a range of columns to be used</option>
30 </param>
31 <when value="cols_number">
32 <param name="cols" type="text" label="Enter column number (separated by a comma)" help="For example : c3,c5,c7"/>
33 </when>
34 <when value="cols_range">
35 <param name="cols" type="text" label="Enter a range of column number, first and last column separated by ':'" help="For example : c2:c7"/>
36 </when>
37 </conditional>
38 <param name="rownames" type="text" value="c1" label="Enter column number containing row labels" help="for example : c1 if labels are in column n°1"/>
39 <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" />
40 <param name="clustering" type="select" label="Clustering method" value="average">
41 <option value="ward.D">Ward</option>
42 <option value="ward.D2">Ward2</option>
43 <option value="single">Single linkage (nearest neighbor)</option>
44 <option value="complete">Complete linkage (farthest neighbor)</option>
45 <option value="average" selected="true">Group average linkage (UPGMA)</option>
46 <option value="mcquitty">Simple average method (WPGMA)</option>
47 <!--option value="median">Median (WPGMC)</option>
48 <option value="centroid">Centroid (UPGMC)</option-->
49 </param>
50 <param name="distance" type="select" label="Distance measurement method" value="euclidean">
51 <option value="euclidean" selected="true">Euclidean</option>
52 <option value="pearson" selected="true">Pearson</option>
53 <option value="spearman">Spearman</option>
54 <option value="kendall">Kendall</option>
55 <option value="maximum">Maximum</option>
56 <option value="manhattan">Manhattan</option>
57 <option value="canberra">Canberra</option>
58 <option value="binary">Binary</option>
59 <option value="minkowski">Minkowski</option>
60 </param>
61 <param name="dendrogram" type="select" label="Apply clustering on :" value="both">
62 <option value="row">Rows</option>
63 <option value="column">Columns</option>
64 <option value="both" selected="true">Rows and columns</option>
65 <option value="none">None</option>
66 </param>
67
68 <param name="output_type" type="select" label="Select output format">
69 <option value="html">html</option>
70 <option value="pdf">pdf</option>
71 <option value="jpeg">jpeg</option>
72 <option value="png">png</option>
73 </param>
74
75 </inputs>
76 <outputs>
77 <data name="output" format="html">
78 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.html" ext="html" visible="true" assign_primary_output="true"/>
79 <filter>output_type=="html"</filter>
80 </data>
81 <data name="pdf" format="pdf">
82 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" ext="pdf" visible="true" assign_primary_output="true"/>
83 <filter>output_type=="pdf"</filter>
84 </data>
85 <data name="jpeg" format="jpg">
86 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.jpg" ext="jpg" visible="true" assign_primary_output="true"/>
87 <filter>output_type=="jpeg"</filter>
88 </data>
89 <data name="png" format="png">
90 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" ext="png" visible="true" assign_primary_output="true"/>
91 <filter>output_type=="png"</filter>
92 </data>
93 </outputs>
94 <tests>
95 <test>
96 <output name="output" file="heatmap.html"/>
97 </test>
98 </tests>
99 <help><![CDATA[
100 **Description**
101
102 This tool allows users to generate, cluster and visualize expression-based heat maps from transcriptomic, proteomic and metabolomic experiments.
103 It is based on heatmaply, an R package for easily creating interactive cluster heatmaps (see reference below)
104
105 -----
106
107 **Input**
108
109 A file (tab-delimited) having a column with labels (e.g. a gene name, Uniprot accession number...) and colums with numerical value (intensities) for clustering.
110 See table below for an example input file
111
112 .. csv-table:: example of input file
113 :header: "Uniprot","iBAQ_CTR1","iBAQ_CTR2","iBAQ_CTR3","iBAQ_pTCN1","iBAQ_pTCN2","iBAQ_pTCN3"
114
115
116 "Q49AN9",17.4091970440807,16.0474907255521,14.9687330755858,21.8454060245779,18.9468529040903,21.2330797498008
117 "O00148",14.1001686145694,14.806777888004,15.3555560564928,17.2942797505583,18.2106568817514,16.9479095182613
118 "F5H6E2",15.0235503328855,16.6142578028388,20.5969569088489,14.6615767253835,17.9752549753108,20.4023495267791
119 "E9PPW7",18.0770953690935,15.312218369812,13.8048301075204,17.5522130063356,15.9664520099065,15.1597932646987
120 "O00483",17.4188205774495,16.783665086968,15.1589556127476,19.7398973660168,20.8648965533665,20.1781898785682
121 "O00571",12.9049717044645,16.717296441372,13.8708732177805,19.8879681981565,21.0815521014477,17.4710040202845
122
123 -----
124
125 **Parameters**
126
127 "Select columns or a range of columns containing expression values": choose the columns to use to perform clustering and to create the heatmap.
128 You can enter specific column number (e.g. c2,c5 will create a heatmap for column 2 and 5 corresponding to condition from the example file above ) or a range of columns to use (e.g. c2:c7 will consider all replicates of each condition in the example above)).
129
130 "Enter column number containing row labels": enter the column number containing the rows labels (e.g. "c1" in the example above).
131
132 "Angle of column labels": In case of long label name, you might want to incline the column labels for practical display.
133
134 "Clustering method": methods for computing hierarchical clustering (six available)
135
136 "Distance measurement method": function used to compute the distance (dissimilarity) between both rows and columns (nine available). The options "pearson", "spearman" and "kendall" can
137 be used to use correlation-based clustering.
138
139 -----
140
141 **Output**
142
143 Default output is html; it allows browsing the heatmap in an interactive way (of note: for large file, display and interactivity can be altered)
144 pdf, jpeg or png format are propsoed for static output.
145
146 -----
147
148 .. class:: infomark
149
150 **Authors**
151 Galili T, O'Callaghan A, Sidi J, Sievert C. heatmaply: an R package for creating interactive cluster heatmaps for online publishing. Bioinformatics. 2018. 34(9):1600-1602. doi: 10.1093/bioinformatics/btx657. PubMed PMID: 29069305
152
153 -----
154
155 .. class:: infomark
156
157 **Galaxy integration**
158
159 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
160
161 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
162
163 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
164
165 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
166
167 ]]></help>
168 </tool>