changeset 4:52b8083a6159 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f

--- a/ggplot_point.xml	Mon Feb 11 17:28:38 2019 -0500
+++ b/ggplot_point.xml	Sun Mar 24 13:21:18 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="ggplot2_point" name="Scatterplot w ggplot2" version="@VERSION@+galaxy0">
+<tool id="ggplot2_point" name="Scatterplot w ggplot2" version="@VERSION@+galaxy1">
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -35,8 +35,10 @@
      color_scale = NULL
      #if $adv.points.pointoptions == "Default"
         gg_point = geom_point(size=1, alpha=1, gg_factor)
+        gg_line = geom_line(size=1, alpha=1, gg_factor)
      #else
         gg_point = geom_point(size='$adv.points.size', alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
+        gg_line = geom_line(size='$adv.points.size', alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
      #end if
 
     names(input)[$adv.factor.factorcol] <- "factor"
@@ -47,14 +49,16 @@
 
     #if $adv.points.pointoptions == "default"
         gg_point = geom_point(size=1, alpha=1, gg_factor)
+        gg_line = geom_line(size=1, alpha=1, gg_factor)
     #else
         gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', gg_factor)
+        gg_line = geom_line(size=$adv.points.size, alpha='$adv.points.alpha', gg_factor)
     #end if
 
-    #if $adv.colors == "Default"
+    #if $adv.factor.colororder == 1
         color_scale = scale_colour_hue(direction='$adv.factor.colororder')
     #else
-        color_scale = scale_color_brewer(palette='$adv.colors', direction='$adv.factor.colororder')
+        color_scale = scale_color_brewer(palette='$adv.factor.colors', direction='$adv.factor.colororder')
     #end if
 
     names(input)[$adv.factor.factorcol] <- "factor"
@@ -65,8 +69,10 @@
 
     #if $adv.points.pointoptions == "default"
         gg_point = geom_point(size=1, alpha=1, gg_factor)
+        gg_line = geom_line(size=1, alpha=1, gg_factor)
     #else
         gg_point = geom_point(size=$adv.points.size, alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
+        gg_line = geom_line(size=$adv.points.size, alpha='$adv.points.alpha', colour='$adv.points.pointcolor')
     #end if
 #end if
 
@@ -104,8 +110,15 @@
     gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
 #end if
 
+## choose between graph types (points/lines/both)
+#if $adv.type == "points"
+    gg_line = NULL
+#elif $adv.type == "lines"
+    gg_point = NULL
+#end if
+
 #this is the actual ggplot command to make the final plot(s)
-plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_facet +
+plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
     gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('$title') + xlab('$xlab') + ylab('$ylab')+
     gg_axistitle + gg_axistext + gg_plottitle + gg_gridline
 
@@ -120,6 +133,11 @@
         <expand macro="title" />
         <expand macro="xy_lab" />
         <section name="adv" title="Advanced Options" expanded="false">
+            <param name="type" type="select" label="Type of plot" >
+                    <option value="points">Points only (default)</option>
+                    <option value="lines">Lines only </option>
+                    <option value="pointslines">Points and Lines</option>
+            </param>
             <conditional name="points">
                 <param name="pointoptions" type="select" label="Data point options">
                     <option value="default" selected="true">Default</option>

--- a/macros.xml	Mon Feb 11 17:28:38 2019 -0500
+++ b/macros.xml	Sun Mar 24 13:21:18 2019 -0400
@@ -136,10 +136,10 @@
                 <!--Do nothing here -->
             </when>
             <when value="Defined">
-                <param name="xaxismin" type="integer" value="0" label="minimal range of x-axis" />
-                <param name="xaxismax" type="integer" value="3" label="maximal range of x-axis" />
-                <param name="yaxismin" type="integer" value="0" label="minimal range of y-axis" />
-                <param name="yaxismax" type="integer" value="3" label="maximal range of y-axis" />
+                <param name="xaxismin" type="float" value="0" label="minimal range of x-axis" />
+                <param name="xaxismax" type="float" value="3" label="maximal range of x-axis" />
+                <param name="yaxismin" type="float" value="0" label="minimal range of y-axis" />
+                <param name="yaxismax" type="float" value="3" label="maximal range of y-axis" />
             </when>
         </conditional>
     </xml>