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comparison galaxy-conf/matrix2png.xml @ 20:9d56b5b85740 draft

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Reuploaded to see if tools get loaded correctly this time.
author timpalpant
date Fri, 15 Jun 2012 15:10:26 -0400
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19:8ad390e82b92 20:9d56b5b85740
1 <tool id="matrix2png" name="Make heatmap" version="1.0.0">
2 <description>using matrix2png</description>
3 <requirement type='package'>matrix2png</requirement>
4 <command>matrix2png -data $input
5 #if str( $range ) != ''
6 -range $range
7 #end if
8
9 -con $con
10 -size $size
11 -numcolors $numcolors
12 -minsize $minsize
13 -mincolor $mincolor
14 -maxcolor $maxcolor
15 -bkgcolor $bkgcolor
16 -missingcolor $missingcolor
17
18 #if str( $map ) != ''
19 -map $map
20 #end if
21
22 #if str( $discrete_color_maps.discrete ) != 'false'
23 -discrete
24 -dmap $dmap
25 #end if
26
27 #if str( $numr ) != ''
28 -numr $numr
29 #end if
30
31 #if str( $numc ) != ''
32 -numc $numc
33 #end if
34
35 -startrow $startrow
36 -startcol $startcol
37
38 #if str( $trim ) != '0'
39 -trim $trim
40 #end if
41
42 #if str( $title ) != ''
43 -title '$title'
44 #end if
45
46 $z $b $d $s $r $c $f $e $l $u
47
48 > $output</command>
49 <inputs>
50 <param name="input" type="data" format="tabular" label="Input data" />
51 <param name="title" type="text" optional="true" size="30" label="Add a title" />
52 <param name="size" type="text" optional="true" value="1:1" label="Pixel dimensions per value as x:y" />
53 <param name="minsize" type="text" optional="true" value="800:600" label="Minimum image size as x:y pixels" />
54 <!-- Not sure what this is, so exclude for now
55 <param name="desctext" type="data" label="Description Text?" /> -->
56 <param name="range" type="text" optional="true" label="Values assigned to mincolor and maxcolor as min:max (default is data range)" />
57 <param name="con" type="float" optional="true" value="1.0" label="Contrast (only applies when not using -range option)" />
58 <param name="numcolors" type="integer" optional="true" value="64" label="Number of colors" />
59 <param name="mincolor" type="text" optional="true" value="blue" label="Color used at lowest value (name or r:g:b triplet)" />
60 <param name="maxcolor" type="text" optional="true" value="yellow" label="Color used at highest value (name or r:g:b triplet)" />
61 <param name="bkgcolor" type="text" optional="true" value="white" label="Color used as background (name or r:g:b triplet)" />
62 <param name="missingcolor" type="text" optional="true" value="grey" label="Color used for missing values (name or r:g:b triplet)" />
63 <param name="map" type="text" optional="true" label="Color choices from preset maps: overrides min/max colors and -b (default = 0 (none))" />
64 <conditional name="discrete_color_maps">
65 <param name="discrete" type="select" label="Use discretized mapping of values to colors">
66 <option value="true">Yes</option>
67 <option value="false" selected="true">No</option>
68 </param>
69 <when value="true">
70 <param name="dmap" type="data" label="Discrete color mapping file to use for discrete mapping (default = preset)" />
71 </when>
72 <when value="false">
73 <!-- No values here -->
74 </when>
75 </conditional>
76 <param name="numr" type="text" optional="true" label="Number of rows to process (default = all)" />
77 <param name="numc" type="text" optional="true" label="Number of columns to process (default = all)" />
78 <param name="startrow" type="integer" optional="true" value="1" label="Index of the first row to be processed" />
79 <param name="startcol" type="integer" optional="true" value="1" label="Index of the first column to be processed" />
80 <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)" />
81 <param name="z" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Row-normalize the data to mean 0 and variance 1" />
82 <param name="b" type="boolean" checked="true" truevalue="-b" falsevalue="" label="Middle of color range is black" />
83 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Add cell dividers" />
84 <param name="s" type="boolean" checked="true" truevalue="-s" falsevalue="" label="Add scale bar" />
85 <param name="r" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Add row names" />
86 <param name="c" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Add column names" />
87 <param name="f" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Data file has a format line" />
88 <param name="e" type="boolean" checked="false" truevalue="-e" falsevalue="" label="Draw ellipses instead of rectangles" />
89 <param name="l" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Log transform the data (base 2)" />
90 <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)" />
91 <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)" />
92 </inputs>
93 <outputs>
94 <data name="output" format="png" />
95 </outputs>
96
97 <help>
98
99 .. class:: warningmark
100
101 This tool requires that matrix2png be installed and available in Galaxy's PATH.
102
103 .. class:: warningmark
104
105 This tool requires tabular data with column AND row headers. For more information about the required format and usage instructions, see the matrix2png_ website.
106
107 .. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html
108
109 .. class:: warningmark
110
111 It is recommended to specify the colorspace range since outliers will often skew it otherwise.
112
113 </help>
114 </tool>