annotate deepTools_macros.xml @ 4:ac935c35437a draft

Uploaded
author bgruening
date Sat, 16 Nov 2013 07:54:13 -0500
parents b5da81864541
children c54d31467be4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
1 <macros>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
2 <macro name="bamCorrelate_mode_actions">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
3 <conditional name="advancedOpt">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
4 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
5 <option value="no" selected="true">no</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
6 <option value="yes">yes</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
7 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
8 <when value="no" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
9 <when value="yes">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
10 <param name="region" type="text" value=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
11 label="Region of the genome to limit the operation to"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
12 help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
13
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
14 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
15 label="Do not extend paired ends"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
16 help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
17
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
18 <param name="ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
19 label="Ignore duplicates"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
20 help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
21
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
22 <param name="minMappingQuality" type="integer" optional="true" value="1" min="1"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
23 label="Minimum mapping quality"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
24 help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
25
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
26 <param name="includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
27 label ="Include zeros"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
28 help ="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
29
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
30 <param name="zMin" type="integer" value="" label="Minimum value for the heatmap intensities"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
31 help="If not specified the value is set automatically."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
32
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
33 <param name="zMax" type="integer" value="" label="Maximum value for the heatmap intensities"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
34 help="If not specified the value is set automatically."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
35
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
36 <expand macro="colormap" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
37 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
38 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
39 </macro>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
40 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
41 <macro name="requirements">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
42 <requirements>
2
b5da81864541 Uploaded
bgruening
parents: 1
diff changeset
43 <requirement type="package" >samtools</requirement>
b5da81864541 Uploaded
bgruening
parents: 1
diff changeset
44 <requirement type="package" >deepTools</requirement>
b5da81864541 Uploaded
bgruening
parents: 1
diff changeset
45 <requirement type="package" >ucsc_tools</requirement>
1
a22ccc261bb3 Uploaded
bgruening
parents: 0
diff changeset
46 <requirement type="package" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">deepTools</requirement>
0
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
47 <requirement type="package" version="0.1">ucsc_tools</requirement>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
48 <requirement type="package" version="1.7.1">numpy</requirement>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
49 <requirement type="package" version="0.7.6">pysam</requirement>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
50 <requirement type="package" version="0.1.19">samtools</requirement>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
51 <yield />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
52 </requirements>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
53 </macro>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
54
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
55 <token name="@REFERENCES@">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
56
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
57 For more informations, please visit our `project site`_.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
58
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
59 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
60
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
61 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
62
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
63
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
64 .. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
65 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
66 .. _project site: https://github.com/fidelram/deepTools
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
67
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
68 </token>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
69
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
70 <macro name="multiple_input_bams">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
71 <repeat name="input_files" title="Input files" min="2">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
72 <param name="bamfile" type="data" format="bam"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
73 label="Bam file"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
74 help="The BAM file must be sorted."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
75 <param name="label" type="text" size="30" optional="true" value=""
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
76 label="Label"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
77 help="Label to use in the output. If not given the dataset name will be used instead."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
78 </repeat>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
79 </macro>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
80
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
81 <token name="@multiple_input_bams@">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
82 #for $i in $input_files:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
83 #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir )
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
84 #set $temp_input_path = $temp_input_handle.name
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
85 #silent $temp_input_handle.close()
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
86 #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path))
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
87 #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path))
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
88 #silent $files.append('%s.bam' % $temp_input_path)
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
89
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
90 ##set $files += [str($i.bamfile)]
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
91 #if str($i.label.value) != "":
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
92 #set $labels += ["\"%s\"" % ($i.label.value)]
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
93 #else
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
94 #set $labels += ["\"%s\"" % ($i.bamfile.name)]
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
95 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
96 #end for
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
97 </token>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
98
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
99 <macro name="reference_genome_source">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
100 <conditional name="source">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
101 <param name="ref_source" type="select" label="Reference genome">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
102 <option value="cached">locally cached</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
103 <option value="history">in your history</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
104 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
105 <when value="cached">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
106 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
107 <options from_data_table="deepTools_seqs" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
108 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
109 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
110 <when value="history">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
111 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
112 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
113 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
114 </macro>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
115
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
116 <token name="@reference_genome_source@">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
117 #if $source.ref_source=="history":
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
118 --genome $source.input1
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
119 #else:
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
120 --genome "${source.input1_2bit.fields.path}"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
121 #end if
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
122 </token>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
123
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
124 <macro name="effectiveGenomeSize">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
125 <conditional name="effectiveGenomeSize">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
126 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
127 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
128 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
129 See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
130 <option value="2150570000">mm9</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
131 <option value="2451960000">hg19</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
132 <option value="121400000">dm3</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
133 <option value="93260000">ce10</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
134 <option value="specific">user specified</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
135 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
136 <when value="specific">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
137 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
138 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
139 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
140 </macro>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
141
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
142 <macro name="graphic_output_settings">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
143 <conditional name="output" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
144 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
145 <option value="no" selected="true">no</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
146 <option value="yes">yes</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
147 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
148 <when value="no" />
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
149 <when value="yes">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
150 <param name="outFileFormat" type="select" label="Image file format">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
151 <option value="png" selected="true">png</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
152 <option value="pdf">pdf</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
153 <option value="svg">svg</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
154 <option value="eps">eps</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
155 <option value="emf">emf</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
156 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
157 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
158 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
159 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
160 </when>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
161 </conditional>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
162 </macro>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
163
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
164 <macro name="colormap">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
165
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
166 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
167 <option value="RdYlBu" selected="true">RdYlBu</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
168 <option value="Accent">Accent</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
169 <option value="Spectral">Spectral</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
170 <option value="Set1">Set1</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
171 <option value="Set2">Set2</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
172 <option value="Set3">Set3</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
173 <option value="Dark2">Dark2</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
174 <option value="Reds">Reds</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
175 <option value="Oranges">Oranges</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
176 <option value="Greens">Greens</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
177 <option value="Blues">Blues</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
178 <option value="Greys">Greys</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
179 <option value="Purples">Purples</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
180 <option value="Paired">Paired</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
181 <option value="Pastel1">Pastel1</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
182 <option value="Pastel2">Pastel2</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
183 <option value="spring">spring</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
184 <option value="summer">summer</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
185 <option value="autumn">autumn</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
186 <option value="winter">winter</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
187 <option value="hot">hot</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
188 <option value="coolwarm">coolwarm</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
189 <option value="cool">cool</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
190 <option value="seismic">seismic</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
191 <option value="terrain">terrain</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
192 <option value="ocean">ocean</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
193 <option value="rainbow">rainbow</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
194 <option value="bone">bone</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
195 <option value="flag">flag</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
196 <option value="prism">prism</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
197 <option value="cubehelix">cubehelix</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
198 <option value="binary">binary</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
199 <option value="pink">pink</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
200 <option value="gray">gray</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
201 <option value="copper">copper</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
202 <option value="BrBG">BrBG</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
203 <option value="BuGn">BuGn</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
204 <option value="BuPu">BuPu</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
205 <option value="GnBu">GnBu</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
206 <option value="OrRd">OrRd</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
207 <option value="PiYG">PiYG</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
208 <option value="PRGn">PRGn</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
209 <option value="PuOr">PuOr</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
210 <option value="PuRd">PuRd</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
211 <option value="PuBu">PuBu</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
212 <option value="RdBu">RdBu</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
213 <option value="RdGy">RdGy</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
214 <option value="RdPu">RdPu</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
215 <option value="YlGn">YlGn</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
216 <option value="PuBuGn">PuBuGn</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
217 <option value="RdYlGn">RdYlGn</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
218 <option value="YlGnBu">YlGnBu</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
219 <option value="YlOrBr">YlOrBr</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
220 <option value="YlOrRd">YlOrRd</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
221 <option value="gist_gray">gist_gray</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
222 <option value="gist_stern">gist_stern</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
223 <option value="gist_earth">gist_earth</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
224 <option value="gist_yarg">gist_yarg</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
225 <option value="gist_ncar">gist_ncar</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
226 <option value="gist_rainbow">gist_rainbow</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
227 <option value="gist_heat">gist_heat</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
228 <option value="gnuplot">gnuplot</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
229 <option value="gnuplot2">gnuplot2</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
230 <option value="CMRmap">CMRmap</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
231 <option value="bwr">bwr</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
232 <option value="hsv">hsv</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
233 <option value="brg">brg</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
234 <option value="jet">jet</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
235 <option value="afmhot">afmhot</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
236 <option value="Accent_r">Accent reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
237 <option value="Spectral_r">Spectral reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
238 <option value="Set1_r">Set1 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
239 <option value="Set2_r">Set2 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
240 <option value="Set3_r">Set3 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
241 <option value="Dark2_r">Dark2 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
242 <option value="Reds_r">Reds reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
243 <option value="Oranges_r">Oranges reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
244 <option value="Greens_r">Greens reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
245 <option value="Blues_r">Blues reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
246 <option value="Greys_r">Greys reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
247 <option value="Purples_r">Purples reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
248 <option value="Paired_r">Paired reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
249 <option value="Pastel1_r">Pastel1 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
250 <option value="Pastel2_r">Pastel2 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
251 <option value="spring_r">spring reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
252 <option value="summer_r">summer reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
253 <option value="autumn_r">autumn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
254 <option value="winter_r">winter reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
255 <option value="hot_r">hot reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
256 <option value="coolwarm_r">coolwarm reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
257 <option value="cool_r">cool reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
258 <option value="seismic_r">seismic reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
259 <option value="terrain_r">terrain reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
260 <option value="ocean_r">ocean reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
261 <option value="rainbow_r">rainbow reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
262 <option value="bone_r">bone reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
263 <option value="flag_r">flag reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
264 <option value="prism_r">prism reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
265 <option value="cubehelix_r">cubehelix reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
266 <option value="binary_r">binary reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
267 <option value="pink_r">pink reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
268 <option value="gray_r">gray reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
269 <option value="copper_r">copper reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
270 <option value="BrBG_r">BrBG reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
271 <option value="BuGn_r">BuGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
272 <option value="BuPu_r">BuPu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
273 <option value="GnBu_r">GnBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
274 <option value="OrRd_r">OrRd reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
275 <option value="PiYG_r">PiYG reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
276 <option value="PRGn_r">PRGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
277 <option value="PuOr_r">PuOr reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
278 <option value="PuRd_r">PuRd reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
279 <option value="PuBu_r">PuBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
280 <option value="RdBu_r">RdBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
281 <option value="RdGy_r">RdGy reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
282 <option value="RdPu_r">RdPu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
283 <option value="YlGn_r">YlGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
284 <option value="PuBuGn_r">PuBuGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
285 <option value="RdYlBu_r">RdYlBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
286 <option value="RdYlGn_r">RdYlGn reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
287 <option value="YlGnBu_r">YlGnBu reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
288 <option value="YlOrBr_r">YlOrBr reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
289 <option value="YlOrRd_r">YlOrRd reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
290 <option value="gist_gray_r">gist_gray reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
291 <option value="gist_stern_r">gist_stern reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
292 <option value="gist_earth_r">gist_earth reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
293 <option value="gist_yarg_r">gist_yarg reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
294 <option value="gist_ncar_r">gist_ncar reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
295 <option value="gist_rainbow_r">gist_rainbow reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
296 <option value="gist_heat_r">gist_heat reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
297 <option value="gnuplot_r">gnuplot reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
298 <option value="gnuplot2_r">gnuplot2 reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
299 <option value="CMRmap_r">CMRmap reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
300 <option value="bwr_r">bwr reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
301 <option value="hsv_r">hsv reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
302 <option value="brg_r">brg reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
303 <option value="jet_r">jet reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
304 <option value="afmhot_r">afmhot reversed</option>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
305 </param>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
306
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
307 </macro>
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
308
d957e25e18a3 Uploaded
bgruening
parents:
diff changeset
309 </macros>