Mercurial > repos > timpalpant > java_genomics_toolkit
comparison galaxy-conf/matrix2png.xml @ 20:9d56b5b85740 draft
Reuploaded to see if tools get loaded correctly this time.
author | timpalpant |
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date | Fri, 15 Jun 2012 15:10:26 -0400 |
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19:8ad390e82b92 | 20:9d56b5b85740 |
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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> |