Mercurial > repos > proteore > proteore_heatmap_visualization

changeset 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
files heatmap.xml heatmap_viz.R
diffstat 2 files changed, 14 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/heatmap.xml	Mon Feb 18 05:58:08 2019 -0500
+++ b/heatmap.xml	Mon Mar 04 08:36:59 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="heatmap" name="HeatMap" version="2019.02.05">
+<tool id="heatmap" name="HeatMap" version="2019.02.26">
     <description></description>
     <requirements>
         <requirement type="package" version="4.7.1">r-plotly</requirement>
@@ -29,13 +29,19 @@
                 <option value="cols_range">Select a range of columns to be used</option>
             </param>
             <when value="cols_number">
-                <param name="cols" type="text" label="Enter column number (separated by a comma)" help="For example : c3,c5,c7"/>
+                <param name="cols" type="text" label="Enter column number (separated by a comma)" help="For example : c3,c5,c7">
+                    <validator type="regex" message="Please enter column numbers, for example: 'c1,c3' for first and third columns">^([c]{0,1}[0-9]+[,]*)+$</validator>
+                </param>
             </when>
             <when value="cols_range">
-                <param name="cols" type="text" label="Enter a range of column number, first and last column separated by ':'" help="For example : c2:c7"/>
+                <param name="cols" type="text" label="Enter a range of column number, first and last column separated by ':'" help="For example : c2:c7">
+                    <validator type="regex" message="Please enter first and last column numbers separated by ':', for example: 'c2:c7' for all colums from the second to the 7th">^[c]{0,1}[0-9]+:[c]{0,1}[0-9]+$</validator>
+                </param>
             </when>
         </conditional>
-        <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"/>
+        <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">
+            <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+        </param>
         <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" />
         <param name="clustering" type="select" label="Clustering method" value="average">
             <option value="ward.D">Ward</option>
@@ -68,8 +74,8 @@
         <param name="output_type" type="select" label="Select output format">
             <option value="html">html</option>
             <option value="pdf">pdf</option>
-            <option value="jpeg">jpeg</option>
-            <option value="png">png</option>
+            <!--option value="jpeg">jpeg</option-->
+            <!--option value="png">png</option-->
         </param>
 
     </inputs>
@@ -140,8 +146,7 @@
 
 **Output**
 
-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, jpeg or png format are propsoed for static output.
+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.
 
 -----
 
--- a/heatmap_viz.R	Mon Feb 18 05:58:08 2019 -0500
+++ b/heatmap_viz.R	Mon Mar 04 08:36:59 2019 -0500
@@ -1,4 +1,5 @@
 #!/usr/bin/Rscript
+options(warn=-1)  #TURN OFF WARNINGS !!!!!!
 
 suppressMessages(library('plotly',quietly = T))
 suppressMessages(library('heatmaply',quietly = T))