--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_generic_x_y_plot.xml	Mon Apr 18 11:11:02 2016 -0400
@@ -0,0 +1,125 @@
+<tool id="plot_generic_x_y_plot" name="Plot generic X-Y plot" version="0.1.0">
+    <description>with R</description>
+
+    <requirements>
+        <requirement type="package" version="3.2.1">R</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+
+    <version_command></version_command>
+
+    <command><![CDATA[
+        Rscript $__tool_directory__/plot_generic_x_y_plot.R
+            --input_file $input_file
+            --header $header
+
+            #if str($output_format)=="pdf"
+                --output_pdf_file $output_pdf_file
+            #else
+                --output_svg_file $output_svg_file
+            #end if
+
+            --x_column_id $x_column_id
+            --y_column_id $y_column_id
+            --xlog $xlog
+            --ylog $ylog
+            --xlab "$xlab"
+            --ylab "$ylab"
+            --col $color
+            --lim $lim
+            --abline $abline
+            --bottom_margin $bottom_margin
+            --left_margin $left_margin
+            --top_margin $top_margin
+            --right_margin $right_margin
+            --pch $pch
+    ]]></command>
+
+    <inputs>
+        <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
+
+        <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
+
+        <param name="output_format" label="Format for output image" type="select" help="">
+            <option value="pdf" selected="True">PDF</option>
+            <option value="svg">SVG</option>
+        </param>
+
+        <param name="x_column_id" type="data_column" data_ref="input_file" label="Column containing data for X axis" multiple="false" numerical="true" help="--x_column_id)"/>
+        <param name="y_column_id" type="data_column" data_ref="input_file" label="Column containing data for Y axis" multiple="false" numerical="true" help="--y_column_id)"/>
+
+        <param name="xlog" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scale with log for X axis?" help="(--xlog)"/>
+        <param name="ylog" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Scale with log for Y axis?" help="(--ylog)"/>
+
+        <param name="xlab" type="text" value="" label="Label for X axis" help="(--xlab)"/>
+        <param name="ylab" type="text" value="" label="Label for Y axis" help="(--ylab)"/>
+
+        <param name="color" label="Color for the points" type="text" value= "grey25" help="R color (--col)"/>
+        <param name="pch" type="integer" value="21" label="Point type" help="(--pch)"/>
+
+        <param name="lim" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Use same limits for both axis?" help="(--lim)"/>
+        <param name="abline" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Add a line for x = y?" help="(--abline)"/>
+
+        <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
+        <param name="left_margin" type="integer" value="5" label="Left margin" help="(--left_margin)"/>
+        <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
+        <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
+    </inputs>
+
+    <outputs>
+        <data name="output_pdf_file" format="pdf"
+            label="${tool.name} on ${on_string}: PDF X-Y plot">
+            <filter>output_format=="pdf"</filter>
+        </data>
+        <data name="output_png_file" format="png"
+            label="${tool.name} on ${on_string}: PNG X-Y plot">
+            <filter>output_format=="png"</filter>
+        </data>
+        <data name="output_svg_file" format="svg"
+            label="${tool.name} on ${on_string}: SVG X-Y plot">
+            <filter>output_format=="svg"</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_file" value="input_file.txt" />
+            <param name="header" value="FALSE" />
+            <param name="output_format" value="pdf" />    
+            <param name="x_column_id" value="2" />
+            <param name="y_column_id" value="3" />
+            <param name="xlog" value="FALSE" />
+            <param name="ylog" value="FALSE" />
+            <param name="xlab" value="" />
+            <param name="ylab" value="" />
+            <param name="color" value= "grey25" />
+            <param name="pch" value="21" />
+            <param name="lim" value="FALSE" />
+            <param name="abline" value="FALSE" />
+            <param name="bottom_margin" value="5" />
+            <param name="left_margin" value="5" />
+            <param name="top_margin" value="1" />
+            <param name="right_margin" value="1" />
+            <output name="output_pdf_file" file="output_file.pdf" />
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool plot a generic X-Y plot:
+
+.. image:: $PATH_TO_IMAGES/output.png
+   :scale: 50 %
+
+This tool relies on R's plot function. The input file must be a tabular file with at least two data columns. The output image is customizable (margin, legend positions, ...) and can be export in different format. 
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
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