--- a/macros.xml	Tue Aug 29 09:02:49 2017 -0400
+++ b/macros.xml	Mon Jun 11 16:05:43 2018 -0400
@@ -9,27 +9,116 @@
     <token name="@VERSION@">2.2.1</token>
 
     <token name="@R_INIT@"><![CDATA[
-## Setup R error handling to go to stderr
-options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
+        ## Setup R error handling to go to stderr
+        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})
 
-## Unify locale settings
-loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+        ## Unify locale settings
+        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
     ]]></token>
 
     <token name="@TRANSFORM@"><![CDATA[
-#if $transform == "log2"
-    input["value"] <- log2(input["value"])
-#elif $transform == "log2plus1"
-    input["value"] <- log2(input["value"]+1)
-#elif $transform == "log10"
-    input["value"] <- log10(input["value"])
-#elif $transform == "log10plus1"
-    input["value"] <- log10(input["value"]+1)
-#end if
+        #if $adv.transform == "log2"
+            input["value"] <- log2(input["value"])
+        #elif $adv.transform == "log2plus1"
+            input["value"] <- log2(input["value"]+1)
+        #elif $adv.transform == "log10"
+            input["value"] <- log10(input["value"])
+        #elif $adv.transform == "log10plus1"
+            input["value"] <- log10(input["value"]+1)
+        #end if
+    ]]></token>
+
+    <token name="@XY_SCALING@"><![CDATA[
+        #Choose between automatically scaled x and y axis or user defined
+        #if $adv.scaling.plot_scaling == "Automatic"
+            gg_scalex = NULL
+            gg_scaley = NULL
+        #else
+            gg_scalex = xlim($adv.scaling.xaxismin, $adv.scaling.xaxismax)
+            gg_scaley = ylim($adv.scaling.yaxismin, $adv.scaling.yaxismax)
+            cat("\n xaxismin: ", $adv.scaling.xaxismin)
+            cat("\n xaxismax: ", $adv.scaling.xaxismax)
+            cat("\n yaxismin: ", $adv.scaling.yaxismin)
+            cat("\n yaxismax: ", $adv.scaling.yaxismax)
+        #end if
+    ]]></token>
+
+    <token name="@THEME@"><![CDATA[
+        ## Choose theme for plot
+        #if $adv.theme == "bw"
+            gg_theme = theme_bw()
+        #else
+            gg_theme = NULL
+        #end if
     ]]></token>
 
+    <token name="@LEGEND@"><![CDATA[
+        ## Show/hide legend
+        #if $adv.legend == "yes"
+            gg_legend = theme(legend.position="right")
+        #else
+            gg_legend = theme(legend.position="none")
+            cat("\n no legend")
+        #end if
+    ]]></token>
+    <token name="@SAVE_OUTPUT@"><![CDATA[
+        ## output options need to be in out section
+        gg_width <- as.double('$out.width_output_dim')
+        gg_height <- as.double('$out.height_output_dim')
+        gg_unit <- '$out.unit_output_dim'
+        gg_dpi <- as.double('$out.dpi_output_dim')
+        gg_add_device <- '$out.additional_output_format'
+        output1 <- '$output1'
+        output2 <- '$output2'
+
+        ## ggsave to png
+        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
+        if(gg_add_device != "none"){
+          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
+        }
+    ]]></token>
+    <xml name="read_complex_input">
+        <param name="input1" type="data" format="tabular" label="Select table"/>
+        <conditional name="inputdata">
+            <param name="input_type" type="select" label="Select input dataset options" help="specific dataset input for reading">
+                <option value="with_header" selected="true">Dataset with header</option>
+                <option value="with_rownames">Dataset with row names</option>
+                <option value="with_header_rownames">Dataset with header and row names</option>
+                <option value="no_header_rownames">Dataset without header or row names</option>
+            </param>
+            <when value="with_header">
+                <param name="header" type="hidden" value="TRUE"/>
+                <param name="row_names_index" type="hidden" value="0"/>
+                <param name="sample_name_orientation" type="select" display="radio" multiple="false" label="Sample names orientation" help="Default horizontal: header names are interpreted as sample names">
+                    <option value="TRUE" selected="true">horizontal</option>
+                    <option value="FALSE">vertial</option>
+                </param>
+            </when>
+            <when value="with_rownames">
+                <param name="header" type="hidden" value="FALSE"/>
+                <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/>
+                <param name="sample_name_orientation" type="select" display="radio" label="Sample names orientation" help="default vertial: row names are interpreted as sample names">
+                    <option value="TRUE">horizontal</option>
+                    <option value="FALSE" selected="true">vertial</option>
+                </param>
+            </when>
+            <when value="with_header_rownames">
+                <param name="header" type="hidden" value="TRUE"/>
+                <param name="row_names_index" type="data_column" data_ref="input1" label="Select column, for row names" help="WARNING: please consider that using row names might shift the grouping columns"/>
+                <param name="sample_name_orientation" type="select" label="Sample names orientation" display="radio" multiple="false" help="deside whether header names or row names are interpreted as sample names">
+                    <option value="TRUE" selected="true">horizontal</option>
+                    <option value="FALSE">vertial</option>
+                </param>
+            </when>
+            <when value="no_header_rownames">
+                <param name="header" type="hidden" value="FALSE"/>
+                <param name="row_names_index" type="hidden" value="0"/>
+                <param name="sample_name_orientation" type="hidden" value="TRUE"/>
+            </when>
+        </conditional>
+    </xml>
     <xml name="transform">
-        <param name="transform" type="select" label="Advanced - log transformation">
+        <param name="transform" type="select" label="Data transformation">
             <option value="none">Plot the data as it is</option>
             <option value="log2">Log2(value) transform my data</option>
             <option value="log2plus1">Log2(value+1) transform my data</option>
@@ -37,23 +126,11 @@
             <option value="log10plus1">Log10(value+1) transform my data</option>
         </param>
     </xml>
-
-    <token name="@XY_SCALING@"><![CDATA[
-#Choose between automatically scaled x and y axis or user defined
-#if $scaling.plot_scaling == "Automatic"
-    gg_scalex = NULL
-    gg_scaley = NULL
-#else
-    gg_scalex = xlim($scaling.xaxismin, $scaling.xaxismax)
-    gg_scaley = ylim($scaling.yaxismin, $scaling.yaxismax)
-#end if
-    ]]></token>
-
     <xml name="xy_scaling">
         <conditional name="scaling">
-            <param name="plot_scaling" type="select" label="Advanced - Axis scaling">
-                <option value="Automatic" selected="True">Automatic axis scaling</option>
-                <option value="Defined">User deined axis scales</option>
+            <param name="plot_scaling" type="select" label="Axis scaling">
+                <option value="Automatic" selected="true">Automatic axis scaling</option>
+                <option value="Defined">User-defined axis scales</option>
             </param>
             <when value="Automatic">
                 <!--Do nothing here -->
@@ -67,33 +144,68 @@
         </conditional>
     </xml>
     <xml name="title">
-        <param name="title" type="text" value="plot title" label="Title of plot" />
+       <param name="title" type="text" value="" label="Plot title">
+            <!--<sanitizer sanitize="false"/> -->
+        </param>
     </xml>
     <xml name="xy_lab">
-        <param name="xlab" type="text" value="title of x-axis" label="Label for x-axis"/>
-        <param name="ylab" type="text" value="title of y-axis" label="Label for y-axis"/> 
+        <param name="xlab" type="text" value="title of x-axis" label="Label for x axis">
+            <sanitizer sanitize="false"/>
+        </param>
+        <param name="ylab" type="text" value="title of y-axis" label="Label for y axis">
+            <sanitizer sanitize="false"/>
+        </param>
+    </xml>
+    <xml name="legend">
+        <param name="legend" type="select" label="Legend options">
+            <option value="yes">Include legend on plot</option>
+            <option value="no">Hide legend</option>
+        </param>
+    </xml>
+    <xml name="theme">
+        <param name="theme" type="select" label="Backgound theme for plot">
+            <option value="bw">Black and white</option>
+            <option value="Default">Default (grey)</option>
+        </param>
     </xml>
     <xml name="dimensions">
-        <param name="with_output_dim" type="float" value="7" label="width of output" help="in inches" />
-        <param name="height_output_dim" type="float" value="7" label="height of output" help="in inches" />
+        <param name="unit_output_dim" type="select" label="Unit of output dimensions" help="default inches">
+            <option value="in" selected="true">Inches (in)</option>
+            <option value="cm">Centimeters (cm)</option>
+            <option value="mm">Millimeters (mm)</option>
+        </param>
+        <param name="width_output_dim" type="float" value="7" label="width of output"/>
+        <param name="height_output_dim" type="float" value="7" label="height of output"/>
+        <param name="dpi_output_dim" type="float" value="300" label="dpi of output" help="Plot resolution. Applies only to raster output types."/>
+        <param name="additional_output_format" type="select" label="Additional output format" help="PNG is always selected as output format">
+            <option value="none" selected="true">only PNG</option>
+            <option value="pdf">PDF</option>
+            <option value="svg">SVG</option>
+            <option value="eps">EPS</option>
+            <option value="ps">PS</option>
+            <option value="tex">TEX (pictex)</option>
+            <option value="jpeg">JPEG</option>
+            <option value="tiff">TIFF</option>
+            <option value="bmp">BMP</option>
+        </param>
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="bibtex">@Book{
+            <citation type="bibtex">@book{wickham2009ggplot2,
                 author = {Hadley Wickham},
                 title = {ggplot2: Elegant Graphics for Data Analysis},
                 publisher = {Springer-Verlag New York},
                 year = {2009},
                 isbn = {978-0-387-98140-6},
-                url = {http://ggplot2.org}
+                url = {http://ggplot2.org},
                 }
             </citation>
+            <yield />
         </citations>
     </xml>
-
-    <xml name="axis_customization" token_label="Advanced - axis title options">
+    <xml name="axis_customization" token_label="Axis title options">
         <param name="axis_customization" type="select" label="@LABEL@">
-            <option value="default" selected="True">Default</option>
+            <option value="default" selected="true">Default</option>
             <option value="defined">User defined label options</option>
         </param>
         <when value="default">
@@ -113,7 +225,7 @@
                 <option value="magenta">Magenta</option>
                 <option value="cyan">Cyan</option>
                 <option value="grey">Grey</option>
-                <option value="gold">Gold</option> 
+                <option value="gold">Gold</option>
             </param>
             <param name="face" type="select" label="Font effect of axis label">
                 <option value="plain">Normal (default)</option>
@@ -122,7 +234,6 @@
             </param>
         </when>
     </xml>
-
     <xml name="colors">
         <param name="colors" type="select" label="Color schemes to differentiate your groups" >
             <option value="Default">Default color scheme</option>
@@ -159,8 +270,22 @@
             <option value="RdBu">Red to blue (discrete, max=11 colors)</option>
             <option value="PuOr">Purple to orange (discrete, max=11 colors)</option>
             <option value="PRGn">Purple to green (discrete, max=11 colors)</option>
-            <option value="BrBG">Brown to teal (discrete, max=11 colors)</option> 
+            <option value="BrBG">Brown to teal (discrete, max=11 colors)</option>
         </param>
     </xml>
-
+    <xml name="additional_output">
+        <data name="output1" format="png" label="${tool.name} on ${on_string}: png"/>
+        <data format="pdf" name="output2" label="${tool.name} on ${on_string}: ${out.additional_output_format}">
+            <change_format>
+                <when input="out.additional_output_format" value="svg" format="svg" />
+                <when input="out.additional_output_format" value="eps" format="eps" />
+                <when input="out.additional_output_format" value="ps" format="ps" />
+                <when input="out.additional_output_format" value="tex" format="txt" />
+                <when input="out.additional_output_format" value="jpeg" format="jpg" />
+                <when input="out.additional_output_format" value="tiff" format="tiff" />
+                <when input="out.additional_output_format" value="bmp" format="bmp" />
+            </change_format>
+            <filter>out['additional_output_format'] != "none"</filter>
+        </data>
+    </xml>
 </macros>