Mercurial > repos > proteore > proteore_heatmap_visualization

comparison heatmap.xml @ 2:99207b432ebc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
author proteore
date Thu, 13 Dec 2018 04:14:21 -0500
parents 4651551b48e4
children 07748b0136bb
comparison
equal deleted inserted replaced
1:4651551b48e4 2:99207b432ebc
1 <tool id="heatmap" name="heatmap visualization from uto table (heatmaply)" version="2018.09.12"> 1 <tool id="heatmap" name="HeatMap" version="2018.12.12">
2 <description></description>
2 <requirements> 3 <requirements>
3 <requirement type="package" version="4.7.1">r-plotly</requirement> 4 <requirement type="package" version="4.7.1">r-plotly</requirement>
4 <requirement type="package" version="0.14.1">r-heatmaply</requirement> 5 <requirement type="package" version="0.14.1">r-heatmaply</requirement>
5 <requirement type="package" version="2.1.1">phantomjs</requirement> 6 <requirement type="package" version="2.1.1">phantomjs</requirement>
6 <requirement type="package" version="2.2.1">pandoc</requirement> 7 <requirement type="package" version="2.2.1">pandoc</requirement>
7 </requirements> 8 </requirements>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 Rscript $__tool_directory__/heatmap_viz.R --input='$file' --output="$file.name" --type='$output_type' --cols='$cols' 10 Rscript $__tool_directory__/heatmap_viz.R
10 --row_names=$rownames --header='$header' --col_text_angle='$angle_col' 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
11 ]]></command> 22 ]]></command>
12 <inputs> 23 <inputs>
13 <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 a file (uto table)" help="" />
14 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" /> 25 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file have a header?" />
15 <param name="cols" type="text" value="" label="Enter columns to use from the first to the last separated by ':'" help='example : 3:8'/> 26 <conditional name="select_data_columns">
16 <param name="rownames" type="integer" value="1" label="Enter the column to use for row labels" help="for example : 1"/> 27 <param name="enter_cols" type="select" label="Select columns or a range of columns to be used for heatmap building">
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 data columns to use for the heatmap separated by commas" help="For example : c3,c5,c7"/>
33 </when>
34 <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"/>
36 </when>
37 </conditional>
38 <param name="rownames" type="text" value="c1" label="Enter the column to use for row labels" help="for example : c1"/>
39 <param name="distance" type="select" label="Distance measurement method" value="euclidean">
40 <option value="euclidean" selected="true">Euclidean</option>
41 <option value="pearson" selected="true">Pearson</option>
42 <option value="spearman">Spearman</option>
43 <option value="kendall">Kendall</option>
44 <option value="maximum">Maximum</option>
45 <option value="manhattan">Manhattan</option>
46 <option value="canberra">Canberra</option>
47 <option value="binary">Binary</option>
48 <option value="minkowski">Minkowski</option>
49 </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">
61 <option value="row">Rows</option>
62 <option value="column">Columns</option>
63 <option value="both" selected="true">Rows and columns</option>
64 <option value="none">None</option>
65 </param>
17 <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" /> 66 <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" />
18 <param name="output_type" type="select" label="Choose the output format"> 67 <param name="output_type" type="select" label="Choose the output format">
19 <option value="html">html</option> 68 <option value="html">html</option>
20 <option value="pdf">pdf</option> 69 <option value="pdf">pdf</option>
21 <option value="jpeg">jpeg</option> 70 <option value="jpeg">jpeg</option>
22 <option value="png">png</option> 71 <option value="png">png</option>
23 </param> 72 </param>
73
24 </inputs> 74 </inputs>
25 <outputs> 75 <outputs>
26 <data name="output" format="html"> 76 <data name="output" format="html">
27 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.html" ext="html" visible="true" assign_primary_output="true"/> 77 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.html" ext="html" visible="true" assign_primary_output="true"/>
28 <filter>output_type=="html"</filter> 78 <filter>output_type=="html"</filter>
44 <test> 94 <test>
45 <output name="output" file="heatmap.html"/> 95 <output name="output" file="heatmap.html"/>
46 </test> 96 </test>
47 </tests> 97 </tests>
48 <help><![CDATA[ 98 <help><![CDATA[
49 Pathview R script
50 Arguments:
51 --help Print this test
52 --input path of the input file (must contains a colum of uniprot and/or geneID accession number)
53 --output Output name of file, could be .png, .jpeg, .pdf or .html
54 --cols Columns to use for heatmap, exemple : '3:8' to use columns from the third to the 8th
55 --row_names Column which contains row names
56 --header True or False
57 --col_text_angle Angle of columns label ; from -90 to 90 degres
58 99
59 Example: 100 This tool creates a heatmap from a tsv file (tab delimited).
60 ./heatmap_viz.R --input='dat.nucl.norm.imputed.tsv' --output='heatmap.html' --cols='3:8' --row_names='2' --header=TRUE --col_text_angle=0 101
102 Input file must have a column for rows labels and colums with numeric data to be used for clustering.
103
104 See table below for an example input file
105
106 .. csv-table:: Example file
107 :header: "Uniprot","iBAQ_CTR1","iBAQ_CTR2","iBAQ_CTR3","iBAQ_pTCN1","iBAQ_pTCN2","iBAQ_pTCN3"
108
109
110 "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
112 "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
114 "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
116
117 ~
118
119 You can choose the columns to be used to create the heatmap.
120
121 You can add manually each colums of interest or enter a range of columns to use.
122
123 You then entered the column number of the column you want to be used for the rows labels .
124
125 If you have long string in your header, you might want to incline the column labels for better reading.
126
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.
128
129 You can select pdf, jpeg or png if you want a static output.
130
131 -----
132
133 .. class:: infomark
134
135 **Authors**
136
137 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
138
139 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
140
141 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
142
143 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
61 144
62 ]]></help> 145 ]]></help>
63 <citations> 146 <citations>
64 <citation type="bibtex"> 147 <citation type="bibtex">
65 @misc{renameTODO, 148 @misc{renameTODO,