Mercurial > repos > timpalpant > java_genomics_toolkit
diff galaxy-conf/matrix2png.xml @ 20:9d56b5b85740 draft
Reuploaded to see if tools get loaded correctly this time.
author | timpalpant |
---|---|
date | Fri, 15 Jun 2012 15:10:26 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-conf/matrix2png.xml Fri Jun 15 15:10:26 2012 -0400 @@ -0,0 +1,114 @@ +<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>