annotate galaxy-conf/matrix2png.xml @ 18:b2a69d34385a draft

Performance improvements to Wig file checksumming. Bug fix in Autocorrelation tool.

<tool id="matrix2png" name="Make heatmap" version="1.0.0">
  <description>using matrix2png</description>
  <requirement type='package'>matrix2png</requirement>
  <command>matrix2png -data $input 
    #if str( $range ) != ''
      -range $range
    #end if
    
    -con $con
    -size $size
    -numcolors $numcolors
    -minsize $minsize
    -mincolor $mincolor
    -maxcolor $maxcolor
    -bkgcolor $bkgcolor
    -missingcolor $missingcolor
    
    #if str( $map ) != ''
      -map $map
    #end if
    
    #if str( $discrete_color_maps.discrete ) != 'false'
      -discrete
      -dmap $dmap
    #end if
    
    #if str( $numr ) != ''
      -numr $numr
    #end if
    
    #if str( $numc ) != ''
      -numc $numc
    #end if
    
    -startrow $startrow
    -startcol $startcol
    
    #if str( $trim ) != '0'
      -trim $trim
    #end if
    
    #if str( $title ) != ''
      -title '$title'
    #end if
    
    $z $b $d $s $r $c $f $e $l $u
    
    > $output</command>
  <inputs>
    <param name="input" type="data" format="tabular" label="Input data" />
    <param name="title" type="text" optional="true" size="30" label="Add a title" />
    <param name="size" type="text" optional="true" value="1:1" label="Pixel dimensions per value as x:y" />
    <param name="minsize" type="text" optional="true" value="800:600" label="Minimum image size as x:y pixels" />
    <!-- Not sure what this is, so exclude for now
    <param name="desctext" type="data" label="Description Text?" /> -->
    <param name="range" type="text" optional="true" label="Values assigned to mincolor and maxcolor as min:max (default is data range)" />
    <param name="con" type="float" optional="true" value="1.0" label="Contrast (only applies when not using -range option)" />
    <param name="numcolors" type="integer" optional="true" value="64" label="Number of colors" />
    <param name="mincolor" type="text" optional="true" value="blue" label="Color used at lowest value (name or r:g:b triplet)" />
    <param name="maxcolor" type="text" optional="true" value="yellow" label="Color used at highest value (name or r:g:b triplet)" />
    <param name="bkgcolor" type="text" optional="true" value="white" label="Color used as background (name or r:g:b triplet)" />
    <param name="missingcolor" type="text" optional="true" value="grey" label="Color used for missing values (name or r:g:b triplet)" />
    <param name="map" type="text" optional="true" label="Color choices from preset maps: overrides min/max colors and -b (default = 0 (none))" />
    <conditional name="discrete_color_maps">
      <param name="discrete" type="select" label="Use discretized mapping of values to colors">
        <option value="true">Yes</option>
        <option value="false" selected="true">No</option>
      </param>
      <when value="true">
        <param name="dmap" type="data" label="Discrete color mapping file to use for discrete mapping (default = preset)" />
      </when>
      <when value="false">
        <!-- No values here -->
      </when>
    </conditional>
    <param name="numr" type="text" optional="true" label="Number of rows to process (default = all)" />
    <param name="numc" type="text" optional="true" label="Number of columns to process (default = all)" />
    <param name="startrow" type="integer" optional="true" value="1" label="Index of the first row to be processed" />
    <param name="startcol" type="integer" optional="true" value="1" label="Index of the first column to be processed" />
    <param name="trim" type="integer" optional="true" value="0" label="Trim this percent of data extremes when determining data range (only without the -range option)" />
    <param name="z" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Row-normalize the data to mean 0 and variance 1" />
    <param name="b" type="boolean" checked="true" truevalue="-b" falsevalue="" label="Middle of color range is black" />
    <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Add cell dividers" />
    <param name="s" type="boolean" checked="true" truevalue="-s" falsevalue="" label="Add scale bar" />
    <param name="r" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Add row names" />
    <param name="c" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Add column names" />
    <param name="f" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Data file has a format line" />
    <param name="e" type="boolean" checked="false" truevalue="-e" falsevalue="" label="Draw ellipses instead of rectangles" />
    <param name="l" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Log transform the data (base 2)" />
    <param name="u" type="boolean" checked="false" truevalue="-u" falsevalue="" label="Put the column labels under the picture instead of above (ignored unless column names)" />
    <param name="g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Put the row labels to the left instead of the right (ignored unless row names)" />
  </inputs>
  <outputs>
    <data name="output" format="png" />
  </outputs>
  
  <help>
    
.. class:: warningmark

This tool requires that matrix2png be installed and available in Galaxy's PATH.

.. class:: warningmark

This tool requires tabular data with column AND row headers. For more information about the required format and usage instructions, see the matrix2png_ website.

.. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html

.. class:: warningmark

It is recommended to specify the colorspace range since outliers will often skew it otherwise.

  </help>
</tool>