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comparison deepTools_macros.xml.orig @ 1:011ea45dda07 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author bgruening
date Mon, 15 Feb 2016 10:25:00 -0500
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0:bb2b0ad44c0e 1:011ea45dda07
1 <macros>
2
3 <xml name="advancedOpt_scaffold">
4 <conditional name="advancedOpt">
5 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
6 <option value="no" selected="true">no</option>
7 <option value="yes">yes</option>
8 </param>
9 <when value="no" />
10 <when value="yes">
11 <yield/>
12 </when>
13 </conditional>
14 </xml>
15
16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
20 --extendReads
21 #end if
22 $advancedOpt.ignoreDuplicates
23 $advancedOpt.centerReads
24 #if $advancedOpt.minMappingQuality:
25 --minMappingQuality '$advancedOpt.minMappingQuality'
26 #end if
27 #if $advancedOpt.samFlagInclude:
28 --samFlagInclude $advancedOpt.samFlagInclude
29 #end if
30 #if $advancedOpt.samFlagExclude:
31 --samFlagExclude $advancedOpt.samFlagExclude
32 #end if
33 </token>
34
35 <xml name="heatmap_options">
36 <expand macro="zMin_zMax" />
37 <expand macro="colorMap" />
38 <expand macro="plotTitle" />
39 <expand macro="plotNumbers" />
40 </xml>
41
42 <token name="@HEATMAP_OPTIONS@">
43 #if str($plotting_type.zMin) != "":
44 --zMin $plotting_type.zMin
45 #end if
46 #if str($plotting_type.zMax) != "":
47 --zMax $plotting_type.zMax
48 #end if
49 --colorMap '$plotting_type.colorMap'
50 $plotting_type.plotNumbers
51 --plotTitle '$plotting_type.plotTitle'
52 </token>
53
54
55 <xml name="includeZeros">
56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
57 label="Include zeros"
58 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
59 </xml>
60
61 <xml name="zMin_zMax">
62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
63 help="If not specified the value is set automatically."/>
64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
65 help="If not specified the value is set automatically."/>
66 </xml>
67
68 <xml name="region_limit_operation">
69 <param argument="--region" type="text" value=""
70 label="Region of the genome to limit the operation to"
71 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
72 </xml>
73
74 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
75 <<<<<<< HEAD
76 <token name="@WRAPPER_VERSION@">2.0.1.0</token>
77 =======
78 <token name="@WRAPPER_VERSION@">2.1.0</token>
79 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
80 <xml name="requirements">
81 <requirements>
82 <requirement type="package" version="2.7.10">python</requirement>
83 <requirement type="binary">@BINARY@</requirement>
84 <<<<<<< HEAD
85 <requirement type="package" version="2.0.1">deepTools</requirement>
86 =======
87 <requirement type="package" version="2.1.0">deepTools</requirement>
88 >>>>>>> d56067f86089e75354a2fad266002db3730766d9
89 <yield />
90 </requirements>
91 <expand macro="stdio" />
92 <version_command>@BINARY@ --version</version_command>
93 </xml>
94
95 <xml name="smoothLength">
96 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
97 label="Smooth values using the following length (in bases)"
98 help ="The smooth length defines a window, larger than the bin size, over which the number of reads is to be averaged. For example, if the bin size is set to 20 and the smooth length is 60, then, for each bin, its value is set to the average of it and its left and right neighbors. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
99 </xml>
100
101
102 <xml name="kmeans_clustering">
103 <conditional name="used_multiple_regions">
104 <param name="used_multiple_regions_options" type="select"
105 label="Did you compute the matrix with more than one groups of regions?"
106 help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
107 <option value="yes">Yes, I used multiple groups of regions</option>
108 <option value="no">No, I used only one group</option>
109 </param>
110 <when value="no">
111 <conditional name="clustering">
112 <param name="clustering_options" type="select" label="Clustering algorithm">
113 <option value="none">No clustering</option>
114 <option value="kmeans">Kmeans clustering</option>
115 <option value="hclust">Hierarchical clustering</option>
116 </param>
117 <when value="kmeans">
118 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
119 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
120 This only works for data that is not grouped, otherwise only the first group will be clustered.
121 If more specific clustering methods are required it is advisable to save the underlying matrix and
122 run the clustering using other software."/>
123 </when>
124 <when value="hclust">
125 <param name="n_hclust" type="integer" value="0" label="number of clusters to compute."
126 help="WARNING: This option causes the tool to run for a very long time! When this option is
127 set, the matrix is split into clusters using the hierarchical clustering algorithm, using ward linkage.
128 This only works for data that is not grouped, otherwise only the first group will be clustered.
129 Note that you must have used the '--missingDataAsZero' option within computeMatrix!
130 If more specific clustering methods are required it is advisable to save the underlying matrix and
131 run the clustering using other software."/>
132 </when>
133 <when value="none" />
134 </conditional>
135 </when>
136 <when value="yes" />
137 </conditional>
138 </xml>
139
140 <token name="@KMEANS_CLUSTERING@">
141 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
142 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
143 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
144 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
145 #end if
146 #end if
147 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'hclust':
148 #if int($advancedOpt.used_multiple_regions.clustering.n_hclust) > 0:
149 --hclust $advancedOpt.used_multiple_regions.clustering.n_hclust
150 #end if
151 #end if
152 #end if
153 </token>
154
155 <xml name="samFlags">
156 <param argument="--samFlagInclude" type="integer" optional="True" value=""
157 label="Include reads based on the SAM flag"
158 help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/>
159 <param argument="--samFlagExclude" type="integer" optional="True" value=""
160 label="Exclude reads based on the SAM flag"
161 help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
162 </xml>
163
164 <xml name="read_processing_options">
165 <expand macro="extendReads" />
166 <expand macro="ignoreDuplicates" />
167 <expand macro="centerReads" />
168 <expand macro="minMappingQuality" />
169 <expand macro="samFlags" />
170 </xml>
171
172 <xml name="plotNumbers">
173 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
174 label="Plot the correlation value"
175 help="If set, then the correlation number is plotted on top of the heatmap."/>
176 </xml>
177
178 <xml name="extendReads">
179 <conditional name="doExtendCustom">
180 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
181 help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
182 By default *each* read mate is extended.
183 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
184 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
185 Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
186 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
187 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
188 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
189 <option value="custom">A custom length, which will be applied to ALL reads.</option>
190 </param>
191 <when value="no" />
192 <when value="yes" />
193 <when value="custom">
194 <param name="extendReadsValue" type="integer" value="300" min="1"
195 label="Extend reads to the given average fragment size"
196 help="Extend all reads to this length" />
197 </when>
198 </conditional>
199 </xml>
200
201 <xml name="corMethod">
202 <param argument="--corMethod" type="select" label="Correlation method">
203 <option value="spearman" selected="True">Spearman</option>
204 <option value="pearson">Pearson</option>
205 </param>
206 </xml>
207
208 <xml name="distanceBetweenBins">
209 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
210 label="Distance between bins"
211 help="By default, multiBamSummary considers consecutive bins of
212 the specified 'Bin size'. However, to reduce the
213 computation time, a larger distance between bins can
214 be given. Larger distances result in fewer bins being
215 considered."/>
216 </xml>
217
218 <xml name="centerReads">
219 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
220 label="Center regions with respect to the fragment length"
221 help="For paired-end data the fragment is defined by the bounds of the reads. For single-end data the bounds are defined by the read and the user-definable fragment/extension length. This option is useful to get a sharper signal around enriched regions."/>
222 </xml>
223
224 <xml name="ignoreDuplicates">
225 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
226 label="Ignore duplicates"
227 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." />
228 </xml>
229
230 <xml name="sortUsing">
231 <param argument="--sortUsing" type="select" label="Method used for sorting"
232 help="For each row the method is computed.">
233 <option value="mean" selected="true">mean</option>
234 <option value="median">median</option>
235 <option value="min">min</option>
236 <option value="max">max</option>
237 <option value="sum">sum</option>
238 <option value="region_length">region length</option>
239 </param>
240 </xml>
241
242 <xml name="sortRegions">
243 <param argument="--sortRegions" type="select" label="Sort regions"
244 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
245 <option value="no">no ordering</option>
246 <option value="descend" selected="true">descending order</option>
247 <option value="ascend">ascending order</option>
248 </param>
249 </xml>
250
251 <xml name="minMappingQuality">
252 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
253 label="Minimum mapping quality"
254 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
255 </xml>
256
257 <xml name="skipZeros">
258 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
259 label ="Skip zeros"
260 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />
261 </xml>
262
263 <xml name="fragmentLength">
264 <param argument="--fragmentLength" type="integer" value="300" min="1"
265 label="Fragment length used for the sequencing"
266 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
267 </xml>
268
269 <xml name="scaleFactor">
270 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
271 help="When used in combination with --normalizeTo1x or
272 --normalizeUsingRPKM, the computed scaling factor will
273 be multiplied by the given scale factor." />
274 </xml>
275
276 <xml name="scaleFactors">
277 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
278 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
279 </xml>
280
281 <xml name="stdio">
282 <stdio>
283 <exit_code range="1:" />
284 <exit_code range=":-1" />
285 <regex match="Error:" />
286 <regex match="Exception:" />
287 <regex match="EXception:" />
288 <regex match="Traceback" />
289 </stdio>
290 </xml>
291
292 <xml name="pseudocount">
293 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
294 </xml>
295
296 <token name="@REFERENCES@">
297
298 .. class:: infomark
299
300 For more information on the tools, please visit our `help site`_.
301
302 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
303
304 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
305
306 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
307 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
308 .. _help site: https://deeptools.readthedocs.org/
309
310 </token>
311 <xml name="citations">
312 <citations>
313 <citation type="doi">10.1093/nar/gku365</citation>
314 <yield />
315 </citations>
316 </xml>
317
318 <xml name="multiple_input_bams">
319 <param argument="--bamfiles" type="data" format="bam" min="2"
320 label="Bam file" multiple="true"
321 help="The BAM file must be sorted."/>
322 </xml>
323
324 <xml name="multiple_input_bigwigs">
325 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
326 label="Bigwig file"
327 help="A Bigwig file."/>
328 </xml>
329
330 <xml name="plotTitle">
331 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
332 label="Title of the plot"
333 help="Title of the plot, to be printed on top of the generated image." />
334 </xml>
335
336
337 <token name="@multiple_input_bams@">
338 <![CDATA[
339 #set files=[]
340 #set labels=[]
341 #for $counter, $bamfile in enumerate($bamfiles):
342 ln -s "${bamfile}" "./${counter}.bam" &&
343 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
344 #silent $files.append('%s.bam' % $counter)
345 #silent $labels.append('%s' % ($bamfile.display_name))
346 #end for
347 ]]>
348 </token>
349
350 <token name="@multiple_input_bigwigs@">
351 <![CDATA[
352 #set files=[]
353 #set labels=[]
354 #for $counter, $bigwig in enumerate($bigwigfiles):
355 ln -s "${bigwig}" "${counter}.bw" &&
356 #silent $files.append('%s.bw' % $counter)
357 #silent $labels.append('%s' % ($bigwig.display_name))
358 #end for
359 ]]>
360 </token>
361
362 <xml name="reference_genome_source">
363 <conditional name="source">
364 <param name="ref_source" type="select" label="Reference genome">
365 <option value="cached">locally cached</option>
366 <option value="history">in your history</option>
367 </param>
368 <when value="cached">
369 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
370 <options from_data_table="lastz_seqs">
371 <filter type="sort_by" column="1" />
372 <validator type="no_options" message="No indexes are available." />
373 </options>
374 </param>
375 </when>
376 <when value="history">
377 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
378 </when>
379 </conditional>
380 </xml>
381
382 <token name="@reference_genome_source@">
383 #if $source.ref_source=="history":
384 --genome $source.input1
385 #else:
386 --genome "$source.input1_2bit.fields.path"
387 #end if
388 </token>
389
390 <xml name="effectiveGenomeSize">
391 <conditional name="effectiveGenomeSize">
392 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
393 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.
394 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
395 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.">
396 <option value="93260000">ce10 (93260000)</option>
397 <option value="121400000">dm3 (121400000)</option>
398 <option value="2451960000" selected="true">hg19 (2451960000)</option>
399 <option value="2150570000">mm9 (2150570000)</option>
400 <option value="specific">user specified</option>
401 </param>
402 <when value="specific">
403 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
404 </when>
405 <when value="2150570000" />
406 <when value="2451960000" />
407 <when value="121400000" />
408 <when value="93260000" />
409 </conditional>
410 </xml>
411
412 <xml name="skipNAs">
413 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
414 label="Ignore missing data?"
415 help="This parameter determines if non-covered regions
416 (regions without overlapping reads) in a bam/bigWig file
417 should be skipped. The default is to treat those
418 regions as having a value of zero. The decision to
419 skip non-covered regions depends on the interpretation
420 of the data. Non-covered regions may represent, for
421 example, repetitive regions that should be ignored.
422 (default: False)" />
423 </xml>
424
425 <xml name="input_save_matrix_values">
426 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
427 </xml>
428
429 <xml name="input_graphic_output_settings">
430 <conditional name="output" >
431 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
432 <option value="no" selected="true">no</option>
433 <option value="yes">yes</option>
434 </param>
435 <when value="no" />
436 <when value="yes">
437 <yield />
438 <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."/>
439 </when>
440 </conditional>
441 </xml>
442
443
444 <xml name="input_image_file_format">
445 <param argument="--outFileFormat" type="select" label="Image file format">
446 <option value="png" selected="true">png</option>
447 <option value="pdf">pdf</option>
448 <option value="svg">svg</option>
449 <option value="eps">eps</option>
450 </param>
451 </xml>
452
453 <xml name="output_image_file_format">
454 <data format="png" name="outFileName" label="${tool.name} image">
455 <change_format>
456 <when input="output.outFileFormat" value="pdf" format="pdf" />
457 <when input="output.outFileFormat" value="svg" format="svg" />
458 <when input="output.outFileFormat" value="eps" format="eps" />
459 </change_format>
460 </data>
461 </xml>
462
463 <xml name="output_image_file_format_not_nested">
464 <data format="png" name="outFileName" label="${tool.name} image">
465 <change_format>
466 <when input="outFileFormat" value="pdf" format="pdf" />
467 <when input="outFileFormat" value="svg" format="svg" />
468 <when input="outFileFormat" value="eps" format="eps" />
469 </change_format>
470 </data>
471 </xml>
472
473 <xml name="output_save_matrix_values">
474 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
475 <filter>
476 ((
477 output['showOutputSettings'] == 'yes' and
478 output['saveMatrix'] is True
479 ))
480 </filter>
481 </data>
482 </xml>
483
484 <xml name="output_graphic_outputs">
485 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
486 <filter>
487 ((
488 output['showOutputSettings'] == 'yes' and
489 output['saveSortedRegions'] is True
490 ))
491 </filter>
492 </data>
493 </xml>
494
495 <xml name="colorMap">
496 <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/">
497 <option value="RdYlBu" selected="true">RdYlBu</option>
498 <option value="Accent">Accent</option>
499 <option value="Spectral">Spectral</option>
500 <option value="Set1">Set1</option>
501 <option value="Set2">Set2</option>
502 <option value="Set3">Set3</option>
503 <option value="Dark2">Dark2</option>
504 <option value="Reds">Reds</option>
505 <option value="Oranges">Oranges</option>
506 <option value="Greens">Greens</option>
507 <option value="Blues">Blues</option>
508 <option value="Greys">Greys</option>
509 <option value="Purples">Purples</option>
510 <option value="Paired">Paired</option>
511 <option value="Pastel1">Pastel1</option>
512 <option value="Pastel2">Pastel2</option>
513 <option value="spring">spring</option>
514 <option value="summer">summer</option>
515 <option value="autumn">autumn</option>
516 <option value="winter">winter</option>
517 <option value="hot">hot</option>
518 <option value="coolwarm">coolwarm</option>
519 <option value="cool">cool</option>
520 <option value="seismic">seismic</option>
521 <option value="terrain">terrain</option>
522 <option value="ocean">ocean</option>
523 <option value="rainbow">rainbow</option>
524 <option value="bone">bone</option>
525 <option value="flag">flag</option>
526 <option value="prism">prism</option>
527 <option value="cubehelix">cubehelix</option>
528 <option value="binary">binary</option>
529 <option value="pink">pink</option>
530 <option value="gray">gray</option>
531 <option value="copper">copper</option>
532 <option value="BrBG">BrBG</option>
533 <option value="BuGn">BuGn</option>
534 <option value="BuPu">BuPu</option>
535 <option value="GnBu">GnBu</option>
536 <option value="OrRd">OrRd</option>
537 <option value="PiYG">PiYG</option>
538 <option value="PRGn">PRGn</option>
539 <option value="PuOr">PuOr</option>
540 <option value="PuRd">PuRd</option>
541 <option value="PuBu">PuBu</option>
542 <option value="RdBu">RdBu</option>
543 <option value="RdGy">RdGy</option>
544 <option value="RdPu">RdPu</option>
545 <option value="YlGn">YlGn</option>
546 <option value="PuBuGn">PuBuGn</option>
547 <option value="RdYlGn">RdYlGn</option>
548 <option value="YlGnBu">YlGnBu</option>
549 <option value="YlOrBr">YlOrBr</option>
550 <option value="YlOrRd">YlOrRd</option>
551 <option value="gist_gray">gist_gray</option>
552 <option value="gist_stern">gist_stern</option>
553 <option value="gist_earth">gist_earth</option>
554 <option value="gist_yarg">gist_yarg</option>
555 <option value="gist_ncar">gist_ncar</option>
556 <option value="gist_rainbow">gist_rainbow</option>
557 <option value="gist_heat">gist_heat</option>
558 <option value="gnuplot">gnuplot</option>
559 <option value="gnuplot2">gnuplot2</option>
560 <option value="CMRmap">CMRmap</option>
561 <option value="bwr">bwr</option>
562 <option value="hsv">hsv</option>
563 <option value="brg">brg</option>
564 <option value="jet">jet</option>
565 <option value="afmhot">afmhot</option>
566 <option value="Accent_r">Accent reversed</option>
567 <option value="Spectral_r">Spectral reversed</option>
568 <option value="Set1_r">Set1 reversed</option>
569 <option value="Set2_r">Set2 reversed</option>
570 <option value="Set3_r">Set3 reversed</option>
571 <option value="Dark2_r">Dark2 reversed</option>
572 <option value="Reds_r">Reds reversed</option>
573 <option value="Oranges_r">Oranges reversed</option>
574 <option value="Greens_r">Greens reversed</option>
575 <option value="Blues_r">Blues reversed</option>
576 <option value="Greys_r">Greys reversed</option>
577 <option value="Purples_r">Purples reversed</option>
578 <option value="Paired_r">Paired reversed</option>
579 <option value="Pastel1_r">Pastel1 reversed</option>
580 <option value="Pastel2_r">Pastel2 reversed</option>
581 <option value="spring_r">spring reversed</option>
582 <option value="summer_r">summer reversed</option>
583 <option value="autumn_r">autumn reversed</option>
584 <option value="winter_r">winter reversed</option>
585 <option value="hot_r">hot reversed</option>
586 <option value="coolwarm_r">coolwarm reversed</option>
587 <option value="cool_r">cool reversed</option>
588 <option value="seismic_r">seismic reversed</option>
589 <option value="terrain_r">terrain reversed</option>
590 <option value="ocean_r">ocean reversed</option>
591 <option value="rainbow_r">rainbow reversed</option>
592 <option value="bone_r">bone reversed</option>
593 <option value="flag_r">flag reversed</option>
594 <option value="prism_r">prism reversed</option>
595 <option value="cubehelix_r">cubehelix reversed</option>
596 <option value="binary_r">binary reversed</option>
597 <option value="pink_r">pink reversed</option>
598 <option value="gray_r">gray reversed</option>
599 <option value="copper_r">copper reversed</option>
600 <option value="BrBG_r">BrBG reversed</option>
601 <option value="BuGn_r">BuGn reversed</option>
602 <option value="BuPu_r">BuPu reversed</option>
603 <option value="GnBu_r">GnBu reversed</option>
604 <option value="OrRd_r">OrRd reversed</option>
605 <option value="PiYG_r">PiYG reversed</option>
606 <option value="PRGn_r">PRGn reversed</option>
607 <option value="PuOr_r">PuOr reversed</option>
608 <option value="PuRd_r">PuRd reversed</option>
609 <option value="PuBu_r">PuBu reversed</option>
610 <option value="RdBu_r">RdBu reversed</option>
611 <option value="RdGy_r">RdGy reversed</option>
612 <option value="RdPu_r">RdPu reversed</option>
613 <option value="YlGn_r">YlGn reversed</option>
614 <option value="PuBuGn_r">PuBuGn reversed</option>
615 <option value="RdYlBu_r">RdYlBu reversed</option>
616 <option value="RdYlGn_r">RdYlGn reversed</option>
617 <option value="YlGnBu_r">YlGnBu reversed</option>
618 <option value="YlOrBr_r">YlOrBr reversed</option>
619 <option value="YlOrRd_r">YlOrRd reversed</option>
620 <option value="gist_gray_r">gist_gray reversed</option>
621 <option value="gist_stern_r">gist_stern reversed</option>
622 <option value="gist_earth_r">gist_earth reversed</option>
623 <option value="gist_yarg_r">gist_yarg reversed</option>
624 <option value="gist_ncar_r">gist_ncar reversed</option>
625 <option value="gist_rainbow_r">gist_rainbow reversed</option>
626 <option value="gist_heat_r">gist_heat reversed</option>
627 <option value="gnuplot_r">gnuplot reversed</option>
628 <option value="gnuplot2_r">gnuplot2 reversed</option>
629 <option value="CMRmap_r">CMRmap reversed</option>
630 <option value="bwr_r">bwr reversed</option>
631 <option value="hsv_r">hsv reversed</option>
632 <option value="brg_r">brg reversed</option>
633 <option value="jet_r">jet reversed</option>
634 <option value="afmhot_r">afmhot reversed</option>
635 </param>
636
637 </xml>
638
639 </macros>