diff volcanoplot.xml @ 3:6d532d760950 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 16205b1cd782c5a4f7c08af7d4ee50dc5903418b

--- a/volcanoplot.xml	Sun Dec 30 08:03:58 2018 -0500
+++ b/volcanoplot.xml	Tue Feb 12 05:32:23 2019 -0500
@@ -1,9 +1,9 @@
-<tool id="volcanoplot" name="Volcano Plot" version="0.0.2">
+<tool id="volcanoplot" name="Volcano Plot" version="0.0.3">
     <description>create a volcano plot</description>
     <requirements>
-        <requirement type="package" version="3.0.0">r-ggplot2</requirement>
+        <requirement type="package" version="3.1.0">r-ggplot2</requirement>
         <requirement type="package" version="0.8.0">r-ggrepel</requirement>
-        <requirement type="package" version="0.7.6">r-dplyr</requirement>
+        <requirement type="package" version="0.7.8">r-dplyr</requirement>
         <requirement type="package" version="1.20.2">r-getopt</requirement>
     </requirements>
     <version_command><![CDATA[
@@ -29,6 +29,9 @@
     #else
         -t 0
     #end if
+    #if $plot_options.boxes:
+        -b
+    #end if
     #if $plot_options.title:
         -T '$plot_options.title'
     #end if
@@ -38,6 +41,15 @@
     #if $plot_options.ylab:
         -Y '$plot_options.ylab'
     #end if
+    #if $plot_options.xmin:
+        -m '$plot_options.xmin'
+    #end if
+    #if $plot_options.xmax:
+        -M '$plot_options.xmax'
+    #end if
+    #if $plot_options.ymax:
+        -W '$plot_options.ymax'
+    #end if
     #if $plot_options.legend:
         -L '$plot_options.legend'
     #end if
@@ -66,9 +78,13 @@
             </when>
         </conditional>
         <section name="plot_options" expanded="false" title="Plot Options">
+            <param name="boxes" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Label Boxes" help="If this is set to Yes, the labels for the points will be in boxes. Default: Yes"/>
             <param name="title" type="text" optional="True" label="Plot title"/>
             <param name="xlab" type="text" optional="True" label="Label for x axis"/>
             <param name="ylab" type="text" optional="True" label="Label for y axis"/>
+            <param name="xmin" type="float" optional="True" label="Minimum value for x axis" help="To customise the x axis limits, specify both minimum and maximum values. Leave empty for automatic values."/>
+            <param name="xmax" type="float" optional="True" label="Maximum value for x axis" help="To customise the x axis limits, specify both minimum and maximum values. Leave empty for automatic values."/>
+            <param name="ymax" type="float" optional="True" label="Maximum value for y axis" help="To customise the y axis upper limit, specify the maximum value, the minimum will be 0. Leave empty for automatic value."/>
             <param name="legend" type="text" optional="True" label="Label for Legend Title"/>
             <param name="legend_labs" type="text" value="Down,Not Sig,Up" label="Labels for Legend" help="Labels in the legend can be specified. Default: Down,Not Sig,Up"/>
         </section>