diff ggplot_histogram.xml @ 2:f52035800250 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf

--- a/ggplot_histogram.xml	Tue Aug 29 09:02:13 2017 -0400
+++ b/ggplot_histogram.xml	Mon Jun 11 16:05:18 2018 -0400
@@ -1,9 +1,10 @@
-<tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@">
+<tool id="ggplot2_histogram" name="Histogram w ggplot2" version="@VERSION@+galaxy0">
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="1.4.2">r-reshape2</requirement>
+        <requirement type="package" version="1.4.3">r-reshape2</requirement>
+        <requirement type="package" version="1.2.1">r-svglite</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 cat '$script' &&
@@ -11,61 +12,59 @@
     ]]></command>
     <configfiles>
         <configfile name="script"><![CDATA[
-
 @R_INIT@
 
 ## Import library
-library("reshape2")
-library("ggplot2")
+library(reshape2)
+library(ggplot2)
 
 integrated <- read.csv('$input1', sep='\t', header=TRUE)
 input <- melt(integrated)
 
-## Show/hide legend
-#if $legend == "yes"
-    gg_legend = NULL
-#else
-    gg_legend = theme(legend.position="none")
-#end if
+@LEGEND@
 
 ## density
-#if $density == "counts"
+#if $adv.density == "counts"
     gg_density = ggplot(input,aes(value, color=variable))
     gg_freq = NULL
-#elif $density == "nfreq"
+#elif $adv.density == "nfreq"
     gg_density = ggplot(input,aes(value, ..ncount.., color=variable))
     gg_freq = NULL
-#elif $density == "freq"
+#elif $adv.density == "freq"
     gg_density = ggplot(input,aes(value, color=variable))
     gg_freq = aes(y=..count../sum(..count..))
 #end if
 
+@TRANSFORM@
+
 @XY_SCALING@
 
-gg_width = $with_output_dim
-gg_height = $height_output_dim
-
+@THEME@
 
-@TRANSFORM@
-
-#if $facet == "facet"
+#if $adv.facet == "facet"
     gg_facet = facet_wrap(~ variable)
 #else
     gg_facet = NULL
 #end if
 
-#if $coloring.colorscheme == "Default"
+#if $adv.coloring.colorscheme == "Default"
     gg_colorscale = NULL
 #else
-    gg_colorscale = scale_color_brewer(palette=$coloring.colors, direction=$coloring.colororder)
+    gg_colorscale = scale_color_brewer(palette=$adv.coloring.colors, direction=$adv.coloring.colororder)
 #end if
 
-gg_density+
-geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size)+gg_facet+gg_colorscale+
-gg_scalex+gg_scaley+theme_bw()+xlab('$xlab')+ylab('$ylab')+gg_legend+ggtitle('$title')
+plot_out <- gg_density +
+    geom_freqpoly(gg_freq, binwidth=$binwidth, size=$size) + gg_facet + gg_colorscale +
+    gg_scalex +
+    gg_scaley +
+    gg_theme +
+    xlab('$xlab') +
+    ylab('$ylab') +
+    gg_legend +
+    ggtitle('$title') +
+    theme(plot.title = element_text(hjust = 0.5))
 
-ggsave(file='Rplot.pdf')
-dev.off()
+@SAVE_OUTPUT@
         ]]></configfile>
     </configfiles>
     <inputs>
@@ -74,54 +73,51 @@
         <expand macro="xy_lab" />
         <param name="size" type="float" value="1.0" label="relative line width" />
         <param name="binwidth" type="float" value="0.5" label="Bin width for plotting"/>
-
-        <expand macro="transform" />
-
-        <param name="density" type="select" label="Advanced - plot counts or density">
-            <option value="counts">Plot counts on the y-axis</option>
-            <option value="freq">Plot frequency on the y-axis</option>
-            <option value="nfreq">Plot normalized frequency on the y-axis</option>
-        </param>
-        <param name="facet" type="select" label="Advanced - faceting">
-            <option value="none">Plot my groups on one plot</option>
-            <option value="facet">Plot my groups on individual plots</option>
-        </param>
-        <conditional name="coloring">
-            <param name="colorscheme" type="select" label="Advanced - coloring groups" >
-                <option value="Default" selected="True">No thanks - just use the default scheme to color code my groups (columns)</option>
-                <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option>
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="density" type="select" label="Plot counts or density">
+                <option value="counts">Plot counts on the y-axis</option>
+                <option value="freq">Plot frequency on the y-axis</option>
+                <option value="nfreq">Plot normalized frequency on the y-axis</option>
+            </param>
+            <param name="facet" type="select" label="Faceting">
+                <option value="none">Plot my groups on one plot</option>
+                <option value="facet">Plot my groups on individual plots</option>
             </param>
-            <when value="Default">
-            </when>
-            <when value="Defined">
-                <expand macro="colors" />
-                <param name="colororder" type="select" label="Reverse color scheme" >
-                    <option value="1">Default order of color scheme</option>
-                    <option value="-1">Reverse the order of my color scheme</option>
-                </param> 
-            </when>
-        </conditional>
-        <expand macro="xy_scaling" />
-        <expand macro="dimensions" />
-        <param name="legend" type="select" label="Legend options">
-            <option value="yes">Include legend on plot</option>
-            <option value="no">Hide legend</option>
-        </param>
+            <conditional name="coloring">
+                <param name="colorscheme" type="select" label="Coloring groups" >
+                    <option value="Default" selected="true">No thanks - just use the default scheme to color code my groups (columns)</option>
+                    <option value="Defined">I want to use defined color palettes to differentiate my groups (columns) </option>
+                </param>
+                <when value="Default">
+                </when>
+                <when value="Defined">
+                    <expand macro="colors" />
+                    <param name="colororder" type="select" label="Reverse color scheme" >
+                        <option value="1">Default order of color scheme</option>
+                        <option value="-1">Reverse the order of my color scheme</option>
+                    </param>
+                </when>
+            </conditional>
+            <expand macro="transform" />
+            <expand macro="xy_scaling" />
+            <expand macro="theme" />
+            <expand macro="legend" />
+        </section>
+        <section name="out" title="Output Options" expanded="true">
+            <expand macro="dimensions" />
+        </section>
     </inputs>
     <outputs>
-        <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/>
-            ToDo: It would be nice to have different output formats for all tools
-        -->
-        <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
+        <expand macro="additional_output" />
     </outputs>
     <tests>
         <test>
             <param name="input1" value="mtcars.txt"/>
-            <output name="output1" file="ggplot_histogram_result1.pdf" compare="sim_size"/>
+            <param name="additional_output_format" value="pdf" />
+            <output name="output2" file="ggplot_histogram_result1.pdf" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
-
 This tool will generate a histogram representing the distrinutions of each numerical column. Each column should have a descriptive header with no spaces, which will be used in the plot legend to represent the corresponding column (group).
 
 Input data example:
@@ -132,7 +128,6 @@
 gene_D  6   9
 gene_E  9   13.5
 gene_F  8   12
-
     ]]></help>
     <expand macro="citations"/>
 </tool>