Mercurial > repos > proteore > proteore_heatmap_visualization

comparison heatmap.xml @ 2:2a04fffda914 draft

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planemo upload commit 4efc56eb769fbceb66c64181441ff8781d523454-dirty
author proteore
date Mon, 04 Mar 2019 08:36:59 -0500
parents b8a5139cf5b9
children 8756766e5b5c
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1:b8a5139cf5b9 2:2a04fffda914
1 <tool id="heatmap" name="HeatMap" version="2019.02.05"> 1 <tool id="heatmap" name="HeatMap" version="2019.02.26">
2 <description></description> 2 <description></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>
27 <param name="enter_cols" type="select" label="Select columns or a range of columns containing expression values"> 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 column number (separated by a comma)" 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]+[,]*)+$</validator>
34 </param>
33 </when> 35 </when>
34 <when value="cols_range"> 36 <when value="cols_range">
35 <param name="cols" type="text" label="Enter a range of column number, first and last column separated by ':'" help="For example : c2:c7"/> 37 <param name="cols" type="text" label="Enter a range of column number, first and last column separated by ':'" help="For example : c2:c7">
38 <validator type="regex" message="Please enter first and last column numbers separated by ':', for example: 'c2:c7' for all colums from the second to the 7th">^[c]{0,1}[0-9]+:[c]{0,1}[0-9]+$</validator>
39 </param>
36 </when> 40 </when>
37 </conditional> 41 </conditional>
38 <param name="rownames" type="text" value="c1" label="Enter column number containing row labels" help="for example : c1 if labels are in column n°1"/> 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">
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>
39 <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" /> 45 <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"> 46 <param name="clustering" type="select" label="Clustering method" value="average">
41 <option value="ward.D">Ward</option> 47 <option value="ward.D">Ward</option>
42 <option value="ward.D2">Ward2</option> 48 <option value="ward.D2">Ward2</option>
43 <option value="single">Single linkage (nearest neighbor)</option> 49 <option value="single">Single linkage (nearest neighbor)</option>
66 </param> 72 </param>
67 73
68 <param name="output_type" type="select" label="Select output format"> 74 <param name="output_type" type="select" label="Select output format">
69 <option value="html">html</option> 75 <option value="html">html</option>
70 <option value="pdf">pdf</option> 76 <option value="pdf">pdf</option>
71 <option value="jpeg">jpeg</option> 77 <!--option value="jpeg">jpeg</option-->
72 <option value="png">png</option> 78 <!--option value="png">png</option-->
73 </param> 79 </param>
74 80
75 </inputs> 81 </inputs>
76 <outputs> 82 <outputs>
77 <data name="output" format="html"> 83 <data name="output" format="html">
138 144
139 ----- 145 -----
140 146
141 **Output** 147 **Output**
142 148
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) 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.
144 pdf, jpeg or png format are propsoed for static output.
145 150
146 ----- 151 -----
147 152
148 .. class:: infomark 153 .. class:: infomark
149 154