Mercurial > repos > proteore > proteore_heatmap_visualization

comparison heatmap.xml @ 3:07748b0136bb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit fb27a6b5de5cd7b269a41be3c85c593b77aa1b18-dirty
author proteore
date Thu, 27 Jun 2019 04:18:07 -0400
parents 99207b432ebc
children
comparison
equal deleted inserted replaced
2:99207b432ebc 3:07748b0136bb
1 <tool id="heatmap" name="HeatMap" version="2018.12.12"> 1 <tool id="heatmap" name="HeatMap" version="2019.06.27">
2 <description></description> 2 <description>(Cluster and visualize the results)</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.7.1">r-plotly</requirement> 4 <requirement type="package" version="4.7.1">r-plotly</requirement>
5 <requirement type="package" version="0.14.1">r-heatmaply</requirement> 5 <requirement type="package" version="0.14.1">r-heatmaply</requirement>
6 <requirement type="package" version="2.1.1">phantomjs</requirement> 6 <requirement type="package" version="2.1.1">phantomjs</requirement>
7 <requirement type="package" version="2.2.1">pandoc</requirement> 7 <requirement type="package" version="2.2.1">pandoc</requirement>
10 Rscript $__tool_directory__/heatmap_viz.R 10 Rscript $__tool_directory__/heatmap_viz.R
11 --input='$file' 11 --input='$file'
12 --output="$file.name" 12 --output="$file.name"
13 --type='$output_type' 13 --type='$output_type'
14 --cols='$select_data_columns.cols' 14 --cols='$select_data_columns.cols'
15 --row_names=$rownames 15 --row_names="$rownames"
16 --header='$header' 16 --header='$header'
17 --col_text_angle='$angle_col' 17 --col_text_angle='$angle_col'
18 --dist="$distance" 18 --dist="$distance"
19 --clust="$clustering" 19 --clust="$clustering"
20 --dendrogram="$dendrogram" 20 --dendrogram="$dendrogram"
21 21
22 ]]></command> 22 ]]></command>
23 <inputs> 23 <inputs>
24 <param name="file" type="data" format="txt,tabular" label="Select a file (uto table)" help="" /> 24 <param name="file" type="data" format="txt,tabular" label="Select your file (table)" help="" />
25 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file have a header?" /> 25 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file contain a header?" />
26 <conditional name="select_data_columns"> 26 <conditional name="select_data_columns">
27 <param name="enter_cols" type="select" label="Select columns or a range of columns to be used for heatmap building"> 27 <param name="enter_cols" type="select" label="Select columns or a range of columns containing expression values">
28 <option value="cols_number">Select columns to be used one by one</option> 28 <option value="cols_number">Select columns to be used one by one</option>
29 <option value="cols_range">Select a range of columns to be used</option> 29 <option value="cols_range">Select a range of columns to be used</option>
30 </param> 30 </param>
31 <when value="cols_number"> 31 <when value="cols_number">
32 <param name="cols" type="text" label="Enter data columns to use for the heatmap separated by commas" help="For example : c3,c5,c7"/> 32 <param name="cols" type="text" label="Enter column number (separated by a comma)" help="For example : c3,c5,c7">
33 <validator type="regex" message="Please enter column numbers, for example: 'c1,c3' for first and third columns">^([c]{0,1}[0-9]+[,]*)+$</validator>
34 </param>
33 </when> 35 </when>
34 <when value="cols_range"> 36 <when value="cols_range">
35 <param name="cols" type="text" label="Enter a range of data columns to use for the heatmap, first and last column separated bay ':'" help="For example : c2:c7"/> 37 <param name="cols" type="text" label="Enter a range of column number, first and last column separated by ':'" help="For example : c2:c7">
38 <validator type="regex" message="Please enter first and last column numbers separated by ':', for example: 'c2:c7' for all colums from the second to the 7th">^[c]{0,1}[0-9]+:[c]{0,1}[0-9]+$</validator>
39 </param>
36 </when> 40 </when>
37 </conditional> 41 </conditional>
38 <param name="rownames" type="text" value="c1" label="Enter the column to use for row labels" help="for example : c1"/> 42 <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 name="distance" type="select" label="Distance measurement method" value="euclidean"> 43 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
44 </param>
45 <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" />
46 <param name="clustering" type="select" label="Clustering method" value="average">
47 <option value="ward.D">Ward</option>
48 <option value="ward.D2">Ward2</option>
49 <option value="single">Single linkage (nearest neighbor)</option>
50 <option value="complete">Complete linkage (farthest neighbor)</option>
51 <option value="average" selected="true">Group average linkage (UPGMA)</option>
52 <option value="mcquitty">Simple average method (WPGMA)</option>
53 <!--option value="median">Median (WPGMC)</option>
54 <option value="centroid">Centroid (UPGMC)</option-->
55 </param>
56 <param name="distance" type="select" label="Distance measurement method" value="euclidean">
40 <option value="euclidean" selected="true">Euclidean</option> 57 <option value="euclidean" selected="true">Euclidean</option>
41 <option value="pearson" selected="true">Pearson</option> 58 <option value="pearson" selected="true">Pearson</option>
42 <option value="spearman">Spearman</option> 59 <option value="spearman">Spearman</option>
43 <option value="kendall">Kendall</option> 60 <option value="kendall">Kendall</option>
44 <option value="maximum">Maximum</option> 61 <option value="maximum">Maximum</option>
45 <option value="manhattan">Manhattan</option> 62 <option value="manhattan">Manhattan</option>
46 <option value="canberra">Canberra</option> 63 <option value="canberra">Canberra</option>
47 <option value="binary">Binary</option> 64 <option value="binary">Binary</option>
48 <option value="minkowski">Minkowski</option> 65 <option value="minkowski">Minkowski</option>
49 </param> 66 </param>
50 <param name="clustering" type="select" label="Clustering method" value="average">
51 <option value="ward.D">Ward</option>
52 <option value="ward.D2">Ward2</option>
53 <option value="single">Single linkage (nearest neighbor)</option>
54 <option value="complete">Complete linkage (farthest neighbor</option>
55 <option value="average" selected="true">Group average linkage (UPGMA)</option>
56 <option value="mcquitty">Simple average method (WPGMA)</option>
57 <!--option value="median">Median (WPGMC)</option>
58 <option value="centroid">Centroid (UPGMC)</option-->
59 </param>
60 <param name="dendrogram" type="select" label="Apply clustering on :" value="both"> 67 <param name="dendrogram" type="select" label="Apply clustering on :" value="both">
61 <option value="row">Rows</option> 68 <option value="row">Rows</option>
62 <option value="column">Columns</option> 69 <option value="column">Columns</option>
63 <option value="both" selected="true">Rows and columns</option> 70 <option value="both" selected="true">Rows and columns</option>
64 <option value="none">None</option> 71 <option value="none">None</option>
65 </param> 72 </param>
66 <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" /> 73
67 <param name="output_type" type="select" label="Choose the output format"> 74 <param name="output_type" type="select" label="Select output format">
68 <option value="html">html</option> 75 <option value="html">html</option>
69 <option value="pdf">pdf</option> 76 <option value="pdf">pdf</option>
70 <option value="jpeg">jpeg</option> 77 <!--option value="jpeg">jpeg</option-->
71 <option value="png">png</option> 78 <!--option value="png">png</option-->
72 </param> 79 </param>
73 80
74 </inputs> 81 </inputs>
75 <outputs> 82 <outputs>
76 <data name="output" format="html"> 83 <data name="output" format="html">
94 <test> 101 <test>
95 <output name="output" file="heatmap.html"/> 102 <output name="output" file="heatmap.html"/>
96 </test> 103 </test>
97 </tests> 104 </tests>
98 <help><![CDATA[ 105 <help><![CDATA[
106 **Description**
99 107
100 This tool creates a heatmap from a tsv file (tab delimited). 108 This tool allows users to generate, cluster and visualize expression-based heat maps from transcriptomic, proteomic and metabolomic experiments.
109 It is based on heatmaply, an R package for easily creating interactive cluster heatmaps (see reference below)
101 110
102 Input file must have a column for rows labels and colums with numeric data to be used for clustering. 111 -----
103 112
113 **Input**
114
115 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.
104 See table below for an example input file 116 See table below for an example input file
105 117
106 .. csv-table:: Example file 118 .. csv-table:: example of input file
107 :header: "Uniprot","iBAQ_CTR1","iBAQ_CTR2","iBAQ_CTR3","iBAQ_pTCN1","iBAQ_pTCN2","iBAQ_pTCN3" 119 :header: "Uniprot","iBAQ_CTR1","iBAQ_CTR2","iBAQ_CTR3","iBAQ_pTCN1","iBAQ_pTCN2","iBAQ_pTCN3"
108 120
109 121
110 "Q49AN9",17.4091970440807,16.0474907255521,14.9687330755858,21.8454060245779,18.9468529040903,21.2330797498008 122 "Q49AN9",17.4091970440807,16.0474907255521,14.9687330755858,21.8454060245779,18.9468529040903,21.2330797498008
111 "O00148",14.1001686145694,14.806777888004,15.3555560564928,17.2942797505583,18.2106568817514,16.9479095182613 123 "O00148",14.1001686145694,14.806777888004,15.3555560564928,17.2942797505583,18.2106568817514,16.9479095182613
112 "F5H6E2",15.0235503328855,16.6142578028388,20.5969569088489,14.6615767253835,17.9752549753108,20.4023495267791 124 "F5H6E2",15.0235503328855,16.6142578028388,20.5969569088489,14.6615767253835,17.9752549753108,20.4023495267791
113 "E9PPW7",18.0770953690935,15.312218369812,13.8048301075204,17.5522130063356,15.9664520099065,15.1597932646987 125 "E9PPW7",18.0770953690935,15.312218369812,13.8048301075204,17.5522130063356,15.9664520099065,15.1597932646987
114 "O00483",17.4188205774495,16.783665086968,15.1589556127476,19.7398973660168,20.8648965533665,20.1781898785682 126 "O00483",17.4188205774495,16.783665086968,15.1589556127476,19.7398973660168,20.8648965533665,20.1781898785682
115 "O00571",12.9049717044645,16.717296441372,13.8708732177805,19.8879681981565,21.0815521014477,17.4710040202845 127 "O00571",12.9049717044645,16.717296441372,13.8708732177805,19.8879681981565,21.0815521014477,17.4710040202845
116 128
117 ~ 129 -----
118 130
119 You can choose the columns to be used to create the heatmap. 131 **Parameters**
120 132
121 You can add manually each colums of interest or enter a range of columns to use. 133 "Select columns or a range of columns containing expression values": choose the columns to use to perform clustering and to create the heatmap.
134 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)).
122 135
123 You then entered the column number of the column you want to be used for the rows labels . 136 "Enter column number containing row labels": enter the column number containing the rows labels (e.g. "c1" in the example above).
124 137
125 If you have long string in your header, you might want to incline the column labels for better reading. 138 "Angle of column labels": In case of long label name, you might want to incline the column labels for practical display.
126 139
127 Default output is html, it allows you to zoom and have row an column labels of a cell by passing your cursor on it. 140 "Clustering method": methods for computing hierarchical clustering (six available)
128 141
129 You can select pdf, jpeg or png if you want a static output. 142 "Distance measurement method": function used to compute the distance (dissimilarity) between both rows and columns (nine available). The options "pearson", "spearman" and "kendall" can
143 be used to use correlation-based clustering.
144
145 -----
146
147 **Output**
148
149 Default output is html; it allows browsing the heatmap in an interactive way (of note: for large file, display and interactivity can be altered), pdf format are proposed for static output.
130 150
131 ----- 151 -----
132 152
133 .. class:: infomark 153 .. class:: infomark
134 154
135 **Authors** 155 **Authors**
156 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
157
158 -----
159
160 .. class:: infomark
161
162 **Galaxy integration**
136 163
137 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 164 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
138 165
139 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform 166 Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
140 167
141 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 168 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
142 169
143 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 170 Help: contact@proteore.org for any questions or concerns about this tool.
144 171
145 ]]></help> 172 ]]></help>
146 <citations>
147 <citation type="bibtex">
148 @misc{renameTODO,
149 author = {LastTODO, FirstTODO},
150 year = {TODO},
151 title = {TODO},
152 url = {https://plot.ly/r/},
153 }</citation>
154 <citation type="bibtex">
155 @misc{renameTODO,
156 author = {LastTODO, FirstTODO},
157 year = {TODO},
158 title = {TODO},
159 url = {https://cran.r-project.org/package=heatmaply},
160 }</citation>
161 </citations>
162 </tool> 173 </tool>