Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/matrix2png.xml @ 25:b43c420a6135 draft default tip

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Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
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20
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1 <tool id="matrix2png" name="Make heatmap" version="1.0.0">
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2 <description>using matrix2png</description>
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3 <requirement type='package'>matrix2png</requirement>
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4 <command>matrix2png -data $input
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5 #if str( $range ) != ''
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6 -range $range
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7 #end if
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8
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9 -con $con
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10 -size $size
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11 -numcolors $numcolors
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12 -minsize $minsize
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13 -mincolor $mincolor
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14 -maxcolor $maxcolor
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15 -bkgcolor $bkgcolor
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16 -missingcolor $missingcolor
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17
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18 #if str( $map ) != ''
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19 -map $map
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20 #end if
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21
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22 #if str( $discrete_color_maps.discrete ) != 'false'
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23 -discrete
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24 -dmap $dmap
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25 #end if
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26
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27 #if str( $numr ) != ''
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28 -numr $numr
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29 #end if
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30
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31 #if str( $numc ) != ''
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32 -numc $numc
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33 #end if
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34
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35 -startrow $startrow
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36 -startcol $startcol
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37
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38 #if str( $trim ) != '0'
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39 -trim $trim
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40 #end if
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41
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42 #if str( $title ) != ''
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43 -title '$title'
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44 #end if
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45
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46 $z $b $d $s $r $c $f $e $l $u
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47
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48 > $output</command>
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49 <inputs>
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50 <param name="input" type="data" format="tabular" label="Input data" />
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51 <param name="title" type="text" optional="true" size="30" label="Add a title" />
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52 <param name="size" type="text" optional="true" value="1:1" label="Pixel dimensions per value as x:y" />
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53 <param name="minsize" type="text" optional="true" value="800:600" label="Minimum image size as x:y pixels" />
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54 <!-- Not sure what this is, so exclude for now
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55 <param name="desctext" type="data" label="Description Text?" /> -->
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56 <param name="range" type="text" optional="true" label="Values assigned to mincolor and maxcolor as min:max (default is data range)" />
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57 <param name="con" type="float" optional="true" value="1.0" label="Contrast (only applies when not using -range option)" />
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58 <param name="numcolors" type="integer" optional="true" value="64" label="Number of colors" />
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59 <param name="mincolor" type="text" optional="true" value="blue" label="Color used at lowest value (name or r:g:b triplet)" />
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60 <param name="maxcolor" type="text" optional="true" value="yellow" label="Color used at highest value (name or r:g:b triplet)" />
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61 <param name="bkgcolor" type="text" optional="true" value="white" label="Color used as background (name or r:g:b triplet)" />
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62 <param name="missingcolor" type="text" optional="true" value="grey" label="Color used for missing values (name or r:g:b triplet)" />
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63 <param name="map" type="text" optional="true" label="Color choices from preset maps: overrides min/max colors and -b (default = 0 (none))" />
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64 <conditional name="discrete_color_maps">
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65 <param name="discrete" type="select" label="Use discretized mapping of values to colors">
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66 <option value="true">Yes</option>
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67 <option value="false" selected="true">No</option>
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68 </param>
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69 <when value="true">
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70 <param name="dmap" type="data" label="Discrete color mapping file to use for discrete mapping (default = preset)" />
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71 </when>
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72 <when value="false">
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73 <!-- No values here -->
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74 </when>
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75 </conditional>
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76 <param name="numr" type="text" optional="true" label="Number of rows to process (default = all)" />
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77 <param name="numc" type="text" optional="true" label="Number of columns to process (default = all)" />
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78 <param name="startrow" type="integer" optional="true" value="1" label="Index of the first row to be processed" />
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79 <param name="startcol" type="integer" optional="true" value="1" label="Index of the first column to be processed" />
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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)" />
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81 <param name="z" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Row-normalize the data to mean 0 and variance 1" />
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82 <param name="b" type="boolean" checked="true" truevalue="-b" falsevalue="" label="Middle of color range is black" />
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83 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Add cell dividers" />
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84 <param name="s" type="boolean" checked="true" truevalue="-s" falsevalue="" label="Add scale bar" />
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85 <param name="r" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Add row names" />
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86 <param name="c" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Add column names" />
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87 <param name="f" type="boolean" checked="false" truevalue="-f" falsevalue="" label="Data file has a format line" />
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88 <param name="e" type="boolean" checked="false" truevalue="-e" falsevalue="" label="Draw ellipses instead of rectangles" />
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89 <param name="l" type="boolean" checked="false" truevalue="-l" falsevalue="" label="Log transform the data (base 2)" />
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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)" />
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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)" />
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92 </inputs>
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93 <outputs>
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94 <data name="output" format="png" />
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95 </outputs>
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96
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97 <help>
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98
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99 .. class:: warningmark
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100
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101 This tool requires that matrix2png be installed and available in Galaxy's PATH.
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102
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103 .. class:: warningmark
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104
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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.
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106
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107 .. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html
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108
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109 .. class:: warningmark
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110
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111 It is recommended to specify the colorspace range since outliers will often skew it otherwise.
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112
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113 </help>
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114 </tool>