Mercurial > repos > proteore > proteore_heatmap_visualization
comparison heatmap.xml @ 2:2a04fffda914 draft
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 |