Mercurial > repos > timpalpant > java_genomics_toolkit

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

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