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planemo upload commit 004439cca3c2fd3b5132eff246d846e5050bfd4f-dirty
author proteore
date Tue, 28 Aug 2018 10:37:03 -0400
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1 <tool id="heatmap" name="heatmap visualization from uto table (heatmaply)" version="0.1.0">
2 <requirements>
3 <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="2.1.1">phantomjs</requirement>
6 <requirement type="package" version="2.2.1">pandoc</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript $__tool_directory__/heatmap_viz.R --input='$file' --output="$file.name" --type='$output_type' --cols='$cols'
10 --row_names=$rownames --header='$header' --col_text_angle='$angle_col'
11 ]]></command>
12 <inputs>
13 <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?" />
15 <param name="cols" type="text" value="" label="Enter columns to use from the first to the last separated by ':'" help='example : 3:8'/>
16 <param name="rownames" type="integer" value="1" label="Enter the column to use for row labels" help="for example : 1"/>
17 <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">
19 <option value="html">html</option>
20 <option value="pdf">pdf</option>
21 <option value="jpeg">jpeg</option>
22 <option value="png">png</option>
23 </param>
24 </inputs>
25 <outputs>
26 <data name="output" format="html">
27 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.html" ext="html" visible="true" assign_primary_output="true"/>
28 <filter>output_type=="html"</filter>
29 </data>
30 <data name="pdf" format="pdf">
31 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" ext="pdf" visible="true" assign_primary_output="true"/>
32 <filter>output_type=="pdf"</filter>
33 </data>
34 <data name="jpeg" format="jpg">
35 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.jpg" ext="jpg" visible="true" assign_primary_output="true"/>
36 <filter>output_type=="jpeg"</filter>
37 </data>
38 <data name="png" format="png">
39 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" ext="png" visible="true" assign_primary_output="true"/>
40 <filter>output_type=="png"</filter>
41 </data>
42 </outputs>
43 <tests>
44 <test>
45 <output name="output" file="heatmap.html"/>
46 </test>
47 </tests>
48 <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
59 Example:
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
61
62 ]]></help>
63 <citations>
64 <citation type="bibtex">
65 @misc{renameTODO,
66 author = {LastTODO, FirstTODO},
67 year = {TODO},
68 title = {TODO},
69 url = {https://plot.ly/r/},
70 }</citation>
71 <citation type="bibtex">
72 @misc{renameTODO,
73 author = {LastTODO, FirstTODO},
74 year = {TODO},
75 title = {TODO},
76 url = {https://cran.r-project.org/package=heatmaply},
77 }</citation>
78 </citations>
79 </tool>