Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/matrix2png.xml @ 12:81d5b81fb3c2 draft
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
| author | timpalpant |
|---|---|
| date | Wed, 25 Apr 2012 16:53:48 -0400 |
| parents | b1952a90d4bf |
| children |
| rev | line source |
|---|---|
| 11 | 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 | |
|
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
99 .. class:: warningmark |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
100 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
101 This tool requires that matrix2png be installed and available in Galaxy's PATH. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
102 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
103 .. class:: warningmark |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
104 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
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. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
106 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
107 .. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
108 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
109 .. class:: warningmark |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
110 |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
111 It is recommended to specify the colorspace range since outliers will often skew it otherwise. |
|
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
112 |
| 11 | 113 </help> |
| 114 </tool> |