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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">
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2 <requirements>
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3 <requirement type="package" version="4.7.1">r-plotly</requirement>
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4 <requirement type="package" version="0.14.1">r-heatmaply</requirement>
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5 <requirement type="package" version="2.1.1">phantomjs</requirement>
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6 <requirement type="package" version="2.2.1">pandoc</requirement>
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7 </requirements>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript $__tool_directory__/heatmap_viz.R --input='$file' --output="$file.name" --type='$output_type' --cols='$cols'
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10 --row_names=$rownames --header='$header' --col_text_angle='$angle_col'
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11 ]]></command>
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12 <inputs>
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13 <param name="file" type="data" format="txt,tabular" label="Select a file (uto table)" help="" />
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14 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
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15 <param name="cols" type="text" value="" label="Enter columns to use from the first to the last separated by ':'" help='example : 3:8'/>
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16 <param name="rownames" type="integer" value="1" label="Enter the column to use for row labels" help="for example : 1"/>
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17 <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" />
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18 <param name="output_type" type="select" label="Choose the output format">
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19 <option value="html">html</option>
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20 <option value="pdf">pdf</option>
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21 <option value="jpeg">jpeg</option>
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22 <option value="png">png</option>
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23 </param>
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24 </inputs>
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25 <outputs>
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26 <data name="output" format="html">
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27 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.html" ext="html" visible="true" assign_primary_output="true"/>
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28 <filter>output_type=="html"</filter>
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29 </data>
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30 <data name="pdf" format="pdf">
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31 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" ext="pdf" visible="true" assign_primary_output="true"/>
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32 <filter>output_type=="pdf"</filter>
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33 </data>
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34 <data name="jpeg" format="jpg">
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35 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.jpg" ext="jpg" visible="true" assign_primary_output="true"/>
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36 <filter>output_type=="jpeg"</filter>
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37 </data>
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38 <data name="png" format="png">
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39 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" ext="png" visible="true" assign_primary_output="true"/>
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40 <filter>output_type=="png"</filter>
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41 </data>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <output name="output" file="heatmap.html"/>
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 Pathview R script
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50 Arguments:
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51 --help Print this test
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52 --input path of the input file (must contains a colum of uniprot and/or geneID accession number)
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53 --output Output name of file, could be .png, .jpeg, .pdf or .html
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54 --cols Columns to use for heatmap, exemple : '3:8' to use columns from the third to the 8th
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55 --row_names Column which contains row names
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56 --header True or False
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57 --col_text_angle Angle of columns label ; from -90 to 90 degres
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58
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59 Example:
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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
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61
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62 ]]></help>
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63 <citations>
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64 <citation type="bibtex">
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65 @misc{renameTODO,
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66 author = {LastTODO, FirstTODO},
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67 year = {TODO},
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68 title = {TODO},
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69 url = {https://plot.ly/r/},
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70 }</citation>
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71 <citation type="bibtex">
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72 @misc{renameTODO,
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73 author = {LastTODO, FirstTODO},
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74 year = {TODO},
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75 title = {TODO},
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76 url = {https://cran.r-project.org/package=heatmaply},
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77 }</citation>
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78 </citations>
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79 </tool>