<tool id="XY_Plot_1" name="Plotting tool" version="1.0.2">
    <description>for multiple series and graph types</description>
    <requirements>
        <requirement type="package" version="3.2.1">R</requirement>
        <requirement type="package" version="2.11.1">fontconfig</requirement>
    </requirements>
    <command interpreter="bash">r_wrapper.sh $script_file</command>
  <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( "${s.input.file_name}", h=${s.header} )
        x${i} = s${i}[,${s.xcol}]
        yrange = 0
        #for $column in str($s.ycol).split(','):
          y${i}${column} = s${i}[,${column}]
          yrange = range(y${i}${column}, yrange, na.rm=TRUE )
        #end for
        xrange = range( x${i}, xrange, na.rm=TRUE )
      #end for
      ## Open output PDF file
      #if $outftype.value == "pdf"
        pdf("outfile.pdf")
      #else
        "${outftype}"( "outfile.${outftype}" , type="cairo")
      #end if
      ## Dummy plot for axis / labels
      plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
      ## Plot each series
      #for $i, $s in enumerate( $series )
        #if $s.series_type['type'] == "line"
          #for $column in str($s.ycol).split(','):
            lines( x${i}, y${i}${column}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} )
          #end for
        #elif $s.series_type.type == "points"
          #for $column in str($s.ycol).split(','):
            points( x${i}, y${i}${column}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} )
          #end for
        #end if
      #end for
      ## Close the PDF file
      devname = dev.off()
    </configfile>
  </configfiles>

  <inputs>
    <param name="main" type="text" value="" label="Plot Title"/>
    <param name="xlab" type="text" value="" label="Label for x axis"/>
    <param name="ylab" type="text" value="" label="Label for y axis"/>
    <param name="outftype" type="select" label="Output File Type">
      <option value="pdf">PDF</option>
      <option value="png">PNG</option>
    </param>
    <repeat name="series" title="Series">
      <param name="input" type="data" format="tabular" label="Dataset"/>
      <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?"/>
      <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
      <param name="ycol" type="data_column" data_ref="input" multiple="true" 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>
  <outputs>
    <data format="pdf" name="out_file_pdf" from_work_dir="outfile.pdf" >
        <filter>(outftype == 'pdf')</filter>
    </data>
    <data format="png" name="out_file_png" from_work_dir="outfile.png">
        <filter>(outftype == 'png')</filter>
    </data>
  </outputs>
    <tests>
        <test>
            <param name="main" value="Example XY Plot"/>
            <param name="xlab" value="Column 1"/>
            <param name="ylab" value="Column 2"/>
            <param name="outftype" value="pdf"/>
            <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_file_pdf" file="XY_Plot_1_out.pdf" ftype="pdf" compare="sim_size" />
        </test>
        <test><!-- test with file with header line, NA values, multiple ycols and PNG output -->
            <param name="main" value="Example XY Plot PNG"/>
            <param name="xlab" value="xlab"/>
            <param name="ylab" value="ylab"/>
            <param name="outftype" value="png"/>
            <param name="series_0|input" value="testinput2.tsv" ftype="tabular"/>
            <param name="series_0|header" value="TRUE"/>
            <param name="series_0|xcol" value="1"/>
            <param name="series_0|ycol" value="2,3"/>
            <param name="series_0|type" value="points"/>
            <param name="series_0|pch" value="1"/>
            <param name="series_0|col" value="2"/>
            <param name="series_0|cex" value="1.0"/>
            <output name="out_file_png" ftype="png" file="testoutput.png" compare="sim_size" />
        </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:: xy_example.jpg
</help>
<citations/>
</tool>