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/tools/plotting/xy_plot.xml

https://bitbucket.org/h_morita_dbcls/galaxy-central
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  1<tool id="XY_Plot_1" name="Plotting tool" version="1.0.1">
  2  <description>for multiple series and graph types</description>
  3  <command interpreter="bash">r_wrapper.sh $script_file</command>
  4
  5  <inputs>
  6    <param name="main" type="text" value="" size="30" label="Plot Title"/>
  7    <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>
  8    <param name="ylab" type="text" value="" size="30" label="Label for y axis"/>
  9    <repeat name="series" title="Series">
 10      <param name="input" type="data" format="tabular" label="Dataset"/>
 11      <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
 12      <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/>
 13      <conditional name="series_type">
 14        <param name="type" type="select" label="Series Type">
 15          <option value="line" selected="true">Line</option>
 16          <option value="points">Points</option>
 17        </param>
 18        <when value="line">
 19          <param name="lty" type="select" label="Line Type">
 20            <option value="1">Solid</option>
 21            <option value="2">Dashed</option>
 22            <option value="3">Dotted</option>
 23          </param>
 24          <param name="col" type="select" label="Line Color">
 25            <option value="1">Black</option>
 26            <option value="2">Red</option>
 27            <option value="3">Green</option>
 28            <option value="4">Blue</option>
 29            <option value="5">Cyan</option>
 30            <option value="6">Magenta</option>
 31            <option value="7">Yellow</option>
 32            <option value="8">Gray</option>
 33          </param>
 34          <param name="lwd" type="float" label="Line Width" value="1.0"/>
 35        </when>
 36        <when value="points">
 37          <param name="pch" type="select" label="Point Type">
 38            <option value="1">Circle (hollow)</option>
 39            <option value="2">Triangle (hollow)</option>
 40            <option value="3">Cross</option>
 41            <option value="4">Diamond (hollow)</option>
 42            <option value="15">Square (filled)</option>
 43            <option value="16">Circle (filled)</option>
 44            <option value="17">Triangle (filled)</option>  
 45          </param>
 46          <param name="col" type="select" label="Point Color">
 47            <option value="1">Black</option>
 48            <option value="2">Red</option>
 49            <option value="3">Green</option>
 50            <option value="4">Blue</option>
 51            <option value="5">Cyan</option>
 52            <option value="6">Magenta</option>
 53            <option value="7">Yellow</option>
 54            <option value="8">Gray</option>
 55          </param>
 56          <param name="cex" type="float" label="Point Scale" value="1.0"/>
 57        </when>
 58      </conditional>
 59    </repeat>       
 60  </inputs>
 61
 62  <configfiles>
 63    <configfile name="script_file">
 64      ## Setup R error handling to go to stderr
 65      options( show.error.messages=F, 
 66               error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
 67      ## Determine range of all series in the plot
 68      xrange = c( NULL, NULL )
 69      yrange = c( NULL, NULL )
 70      #for $i, $s in enumerate( $series )
 71        s${i} = read.table( "${s.input.file_name}" )
 72        x${i} = s${i}[,${s.xcol}]
 73        y${i} = s${i}[,${s.ycol}]
 74        xrange = range( x${i}, xrange )
 75        yrange = range( y${i}, yrange )
 76      #end for
 77      ## Open output PDF file
 78      pdf( "${out_file1}" )
 79      ## Dummy plot for axis / labels
 80      plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
 81      ## Plot each series
 82      #for $i, $s in enumerate( $series )
 83        #if $s.series_type['type'] == "line"
 84          lines( x${i}, y${i}, lty=${s.series_type.lty}, lwd=${s.series_type.lwd}, col=${s.series_type.col} )
 85        #elif $s.series_type.type == "points"
 86          points( x${i}, y${i}, pch=${s.series_type.pch}, cex=${s.series_type.cex}, col=${s.series_type.col} )
 87        #end if
 88      #end for    
 89      ## Close the PDF file
 90      devname = dev.off() 
 91    </configfile>
 92  </configfiles>
 93
 94  <outputs>
 95    <data format="pdf" name="out_file1" />
 96  </outputs>
 97
 98    <tests>
 99        <test>
100            <param name="main" value="Example XY Plot"/>
101            <param name="xlab" value="Column 1"/>
102            <param name="ylab" value="Column 2"/>
103            <param name="input" value="2.tabular" ftype="tabular"/>
104            <param name="xcol" value="1"/>
105            <param name="ycol" value="2"/>
106            <param name="type" value="line"/>
107            <param name="lty" value="2"/>
108            <param name="col" value="2"/>
109            <param name="lwd" value="1.0"/>
110            <output name="out_file1" file="XY_Plot_1_out.pdf"/>
111        </test>
112    </tests>
113<help>
114.. class:: infomark
115
116This 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.
117
118-----
119
120.. class:: warningmark
121
122This 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.
123
124-----
125
126**Example**
127
128Input file::
129
130    1   68  4.1
131    2   71  4.6
132    3   62  3.8
133    4   75  4.4
134    5   58  3.2
135    6   60  3.1
136    7   67  3.8
137    8   68  4.1
138    9   71  4.3
139    10  69  3.7 
140
141Create a two series XY plot on the above data:
142
143- Series 1: Red Dashed-Line plot between columns 1 and 2
144- Series 2: Blue Circular-Point plot between columns 3 and 2 
145
146.. image:: ../static/images/xy_example.jpg
147</help>
148</tool>