<tool id="XY_Plot_1" name="Plotting tool" version="1.0.1">

  <description>for multiple series and graph types</description>

  <command interpreter="bash">r_wrapper.sh $script_file</command>



  <inputs>

    <param name="main" type="text" value="" size="30" label="Plot Title"/>

    <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>

    <param name="ylab" type="text" value="" size="30" label="Label for y axis"/>

    <repeat name="series" title="Series">

      <param name="input" type="data" format="tabular" label="Dataset"/>

      <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>

      <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/>

      <conditional name="series_type">

        <param name="type" type="select" label="Series Type">

          <option value="line" selected="true">Line</option>

          <option value="points">Points</option>

        </param>

        <when value="line">

          <param name="lty" type="select" label="Line Type">

            <option value="1">Solid</option>

            <option value="2">Dashed</option>

            <option value="3">Dotted</option>

          </param>

          <param name="col" type="select" label="Line Color">

            <option value="1">Black</option>

            <option value="2">Red</option>

            <option value="3">Green</option>

            <option value="4">Blue</option>

            <option value="5">Cyan</option>

            <option value="6">Magenta</option>

            <option value="7">Yellow</option>

            <option value="8">Gray</option>

          </param>

          <param name="lwd" type="float" label="Line Width" value="1.0"/>

        </when>

        <when value="points">

          <param name="pch" type="select" label="Point Type">

            <option value="1">Circle (hollow)</option>

            <option value="2">Triangle (hollow)</option>

            <option value="3">Cross</option>

            <option value="4">Diamond (hollow)</option>

            <option value="15">Square (filled)</option>

            <option value="16">Circle (filled)</option>

            <option value="17">Triangle (filled)</option>  

          </param>

          <param name="col" type="select" label="Point Color">

            <option value="1">Black</option>

            <option value="2">Red</option>

            <option value="3">Green</option>

            <option value="4">Blue</option>

            <option value="5">Cyan</option>

            <option value="6">Magenta</option>

            <option value="7">Yellow</option>

            <option value="8">Gray</option>

          </param>

          <param name="cex" type="float" label="Point Scale" value="1.0"/>

        </when>

      </conditional>

    </repeat>       

  </inputs>



  <configfiles>

    <configfile name="script_file">

      ## Setup R error handling to go to stderr

      options( show.error.messages=F, 

               error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )

      ## Determine range of all series in the plot

      xrange = c( NULL, NULL )

      yrange = c( NULL, NULL )

      #for $i, $s in enumerate( $series )

        s${i} = read.table( "${s.input.file_name}" )

        x${i} = s${i}[,${s.xcol}]

        y${i} = s${i}[,${s.ycol}]

        xrange = range( x${i}, xrange )

        yrange = range( y${i}, yrange )

      #end for

      ## Open output PDF file

      pdf( "${out_file1}" )

      ## Dummy plot for axis / labels

      plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )

      ## Plot each series

      #for $i, $s in enumerate( $series )

        #if $s.series_type['type'] == "line"

          lines( x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} )

        #elif $s.series_type.type == "points"

          points( x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} )

        #end if

      #end for    

      ## Close the PDF file

      devname = dev.off() 

    </configfile>

  </configfiles>



  <outputs>

    <data format="pdf" name="out_file1" />

  </outputs>



    <tests>

        <test>

            <param name="main" value="Example XY Plot"/>

            <param name="xlab" value="Column 1"/>

            <param name="ylab" value="Column 2"/>

            <param name="input" value="2.tabular" ftype="tabular"/>

            <param name="xcol" value="1"/>

            <param name="ycol" value="2"/>

            <param name="type" value="line"/>

            <param name="lty" value="2"/>

            <param name="col" value="2"/>

            <param name="lwd" value="1.0"/>

            <output name="out_file1" file="XY_Plot_1_out.pdf"/>

        </test>

    </tests>

<help>

.. class:: infomark



This tool allows you to plot values contained in columns of a dataset against each other and also allows you to have different series corresponding to the same or different datasets in one plot.



-----



.. class:: warningmark



This tool throws an error if the columns selected for plotting are absent or are not numeric and also if the lengths of these columns differ.



-----



**Example**



Input file::



    1   68  4.1

    2   71  4.6

    3   62  3.8

    4   75  4.4

    5   58  3.2

    6   60  3.1

    7   67  3.8

    8   68  4.1

    9   71  4.3

    10  69  3.7 



Create a two series XY plot on the above data:



- Series 1: Red Dashed-Line plot between columns 1 and 2

- Series 2: Blue Circular-Point plot between columns 3 and 2 



.. image:: ../static/images/xy_example.jpg

</help>

</tool>