annotate xy_plot.xml @ 7:afb09b6aee95 draft

Uploaded

<tool id="XY_Plot_1_multiformat" name="Plotting tool" version="1.0.1">
  <description>for multiple series and graph types and multiple output types</description>
  <requirements>
    <requirement type="package" version="3.1.2">R</requirement>
    <requirement type="package" version="2.11.1">fontconfig</requirement>
   </requirements>
  <command interpreter="bash">r_wrapper.sh $script_file</command>

  <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="ftype" type="select" label="File Type">
            <option value="pdf">PDF</option>
            <option value="png">PNG</option>
            <option value="jpeg">JPEG</option>
            <option value="bmp">BMP</option>
            <option value="tiff">TIFF</option>
          </param>
    <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
      #if $ftype.value == "pdf"
        pdf("outfile.pdf")
      #else
        "${ftype}"( "outfile.${ftype}" , type="cairo")
      #end if      
      ## Dummy plot for axis / labels
      plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
      ## Plot each series
      #for $i, $s in enumerate( $series )
        #if $s.series_type['type'] == "line"
          lines( x${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" from_work_dir="outfile.pdf" >
        <filter>(ftype == 'pdf') </filter>
    </data>
    <data format="png" name="out_file2" from_work_dir="outfile.png">
        <filter>(ftype == 'png') </filter>
    </data>    
    <data format="jpg" name="out_file3" from_work_dir="outfile.jpeg">
        <filter>(ftype == 'jpeg') </filter>
    </data>
    <data format="bmp" name="out_file4" from_work_dir="outfile.bmp">
        <filter>(ftype == 'bmp') </filter>
    </data>
    <data format="tiff" name="out_file5" from_work_dir="outfile.tiff">
        <filter>(ftype == 'tiff') </filter>
    </data>
  </outputs>

    <tests>
        <test>
            <param name="main" value="Example XY Plot PDF"/>
            <param name="xlab" value="Column 1"/>
            <param name="ylab" value="Column 2"/>
            <param name="ftype" 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_file1" file="XY_Plot_1_multi_out.pdf" md5="83f82e036bdd7fcd51f29e3b7a05c19b"/>
        </test>
        <test>
            <param name="main" value="Example XY Plot PNG"/>
            <param name="xlab" value="Column 1"/>
            <param name="ylab" value="Column 2"/>
            <param name="ftype" value="png"/>
            <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_file2" file="XY_Plot_1_multi_out.png" md5="777f98fc9a29c3a02ce4da2fa61437c9"/>
        </test>
        <test>
            <param name="main" value="Example XY Plot JPEG"/>
            <param name="xlab" value="Column 1"/>
            <param name="ylab" value="Column 2"/>
            <param name="ftype" value="jpeg"/>
            <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_file3" file="XY_Plot_1_multi_out.jpeg" md5="609f009b8cd92c0662cb39d6e2eb8cc7"/>
        </test>
        <test>
            <param name="main" value="Example XY Plot BMP"/>
            <param name="xlab" value="Column 1"/>
            <param name="ylab" value="Column 2"/>
            <param name="ftype" value="bmp"/>
            <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_file4" file="XY_Plot_1_multi_out.bmp" md5="a036aa3d0bbc0ff58664077cb5c8e04a"/>
        </test>
        <test>
            <param name="main" value="Example XY Plot TIFF"/>
            <param name="xlab" value="Column 1"/>
            <param name="ylab" value="Column 2"/>
            <param name="ftype" value="tiff"/>
            <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_file5" file="XY_Plot_1_multi_out.tiff" md5="e6ba5639144b23480c556e2185bb5d9a"/>
        </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>
</tool>