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comparison deepTools_macros.xml @ 0:14cb57237e46 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:26:32 -0500
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children 275ed3e83de0
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-1:000000000000 0:14cb57237e46
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 <token name="@WRAPPER_VERSION@">2.0.1</token>
76 <xml name="requirements">
77 <requirements>
78 <requirement type="package" version="2.7.10">python</requirement>
79 <requirement type="binary">@BINARY@</requirement>
80 <requirement type="package" version="2.0.1">deepTools</requirement>
81 <yield />
82 </requirements>
83 <expand macro="stdio" />
84 <version_command>@BINARY@ --version</version_command>
85 </xml>
86
87 <xml name="smoothLength">
88 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
89 label="Smooth values using the following length (in bases)"
90 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."/>
91 </xml>
92
93
94 <xml name="kmeans_clustering">
95 <conditional name="used_multiple_regions">
96 <param name="used_multiple_regions_options" type="select"
97 label="Did you compute the matrix with more than one groups of regions?"
98 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.">
99 <option value="yes">Yes, I used multiple groups of regions</option>
100 <option value="no">No, I used only one group</option>
101 </param>
102 <when value="no">
103 <conditional name="clustering">
104 <param name="clustering_options" type="select" label="Clustering algorithm">
105 <option value="none">No clustering</option>
106 <option value="kmeans">Kmeans clustering</option>
107 </param>
108 <when value="kmeans">
109 <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute"
110 help="When this option is set, the matrix is split into clusters using the k-means algorithm.
111 This only works for data that is not grouped, otherwise only the first group will be clustered.
112 If more specific clustering methods are required it is advisable to save the underlying matrix and
113 run the clustering using other software."/>
114 </when>
115 <when value="none" />
116 </conditional>
117 </when>
118 <when value="yes" />
119 </conditional>
120 </xml>
121
122 <token name="@KMEANS_CLUSTERING@">
123 #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
124 #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
125 #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
126 --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
127 #end if
128 #end if
129 #end if
130 </token>
131
132 <xml name="samFlags">
133 <param argument="--samFlagInclude" type="integer" optional="True" value=""
134 label="Include reads based on the SAM flag"
135 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."/>
136 <param argument="--samFlagExclude" type="integer" optional="True" value=""
137 label="Exclude reads based on the SAM flag"
138 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."/>
139 </xml>
140
141 <xml name="read_processing_options">
142 <expand macro="extendReads" />
143 <expand macro="ignoreDuplicates" />
144 <expand macro="centerReads" />
145 <expand macro="minMappingQuality" />
146 <expand macro="samFlags" />
147 </xml>
148
149 <xml name="plotNumbers">
150 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
151 label="Plot the correlation value"
152 help="If set, then the correlation number is plotted on top of the heatmap."/>
153 </xml>
154
155 <xml name="extendReads">
156 <conditional name="doExtendCustom">
157 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
158 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.
159 By default *each* read mate is extended.
160 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
161 Unmated reads, mate reads that map to different chromosomes or too far apart are extended to the given value.
162 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
163 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
164 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
165 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
166 <option value="custom">A custom length, which will be applied to ALL reads.</option>
167 </param>
168 <when value="no" />
169 <when value="yes" />
170 <when value="custom">
171 <param name="extendReadsValue" type="integer" value="300" min="1"
172 label="Extend reads to the given average fragment size"
173 help="Extend all reads to this length" />
174 </when>
175 </conditional>
176 </xml>
177
178 <xml name="corMethod">
179 <param argument="--corMethod" type="select" label="Correlation method">
180 <option value="spearman" selected="True">Spearman</option>
181 <option value="pearson">Pearson</option>
182 </param>
183 </xml>
184
185 <xml name="distanceBetweenBins">
186 <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
187 label="Distance between bins"
188 help="By default, multiBamSummary considers consecutive bins of
189 the specified 'Bin size'. However, to reduce the
190 computation time, a larger distance between bins can
191 be given. Larger distances result in fewer bins being
192 considered."/>
193 </xml>
194
195 <xml name="centerReads">
196 <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
197 label="Center regions with respect to the fragment length"
198 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."/>
199 </xml>
200
201 <xml name="ignoreDuplicates">
202 <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
203 label="Ignore duplicates"
204 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." />
205 </xml>
206
207 <xml name="sortUsing">
208 <param argument="--sortUsing" type="select" label="Method used for sorting"
209 help="For each row the method is computed.">
210 <option value="mean" selected="true">mean</option>
211 <option value="median">median</option>
212 <option value="min">min</option>
213 <option value="max">max</option>
214 <option value="sum">sum</option>
215 <option value="region_length">region length</option>
216 </param>
217 </xml>
218
219 <xml name="sortRegions">
220 <param argument="--sortRegions" type="select" label="Sort regions"
221 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
222 <option value="no">no ordering</option>
223 <option value="descend" selected="true">descending order</option>
224 <option value="ascend">ascending order</option>
225 </param>
226 </xml>
227
228 <xml name="minMappingQuality">
229 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
230 label="Minimum mapping quality"
231 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
232 </xml>
233
234 <xml name="skipZeros">
235 <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
236 label ="Skip zeros"
237 help ="If set, then zero counts that happen for *all* BAM files given are ignored. This may result in fewer considered regions." />
238 </xml>
239
240 <xml name="fragmentLength">
241 <param argument="--fragmentLength" type="integer" value="300" min="1"
242 label="Fragment length used for the sequencing"
243 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."/>
244 </xml>
245
246 <xml name="scaleFactor">
247 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
248 help="When used in combination with --normalizeTo1x or
249 --normalizeUsingRPKM, the computed scaling factor will
250 be multiplied by the given scale factor." />
251 </xml>
252
253 <xml name="scaleFactors">
254 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
255 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
256 </xml>
257
258 <xml name="stdio">
259 <stdio>
260 <exit_code range="1:" />
261 <exit_code range=":-1" />
262 <regex match="Error:" />
263 <regex match="Exception:" />
264 <regex match="EXception:" />
265 <regex match="Traceback" />
266 </stdio>
267 </xml>
268
269 <xml name="pseudocount">
270 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
271 </xml>
272
273 <token name="@REFERENCES@">
274
275 .. class:: infomark
276
277 For more information on the tools, please visit our `help site`_.
278
279 If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com
280
281 This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.
282
283 .. _Bioinformatics and Deep-Sequencing Unit: http://www.ie-freiburg.mpg.de/bioinformaticsfac
284 .. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
285 .. _help site: https://deeptools.readthedocs.org/
286
287 </token>
288 <xml name="citations">
289 <citations>
290 <citation type="doi">10.1093/nar/gku365</citation>
291 <yield />
292 </citations>
293 </xml>
294
295 <xml name="multiple_input_bams">
296 <param argument="--bamfiles" type="data" format="bam" min="2"
297 label="Bam file" multiple="true"
298 help="The BAM file must be sorted."/>
299 </xml>
300
301 <xml name="multiple_input_bigwigs">
302 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
303 label="Bigwig file"
304 help="A Bigwig file."/>
305 </xml>
306
307 <xml name="plotTitle">
308 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
309 label="Title of the plot"
310 help="Title of the plot, to be printed on top of the generated image." />
311 </xml>
312
313 <token name="@multiple_input_bams@">
314 <![CDATA[
315 #set files=[]
316 #set labels=[]
317 #for $counter, $bamfile in enumerate($bamfiles):
318 ln -s "${bamfile}" "./${counter}.bam" &&
319 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
320 #silent $files.append('%s.bam' % $counter)
321 #silent $labels.append('%s' % ($bamfile.display_name))
322 #end for
323 ]]>
324 </token>
325
326 <token name="@multiple_input_bigwigs@">
327 <![CDATA[
328 #set files=[]
329 #set labels=[]
330 #for $counter, $bigwig in enumerate($bigwigfiles):
331 ln -s "${bigwig}" "${counter}.bw" &&
332 #silent $files.append('%s.bw' % $counter)
333 #silent $labels.append('%s' % ($bigwig.display_name))
334 #end for
335 ]]>
336 </token>
337
338 <xml name="reference_genome_source">
339 <conditional name="source">
340 <param name="ref_source" type="select" label="Reference genome">
341 <option value="cached">locally cached</option>
342 <option value="history">in your history</option>
343 </param>
344 <when value="cached">
345 <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
346 <options from_data_table="lastz_seqs">
347 <filter type="sort_by" column="1" />
348 <validator type="no_options" message="No indexes are available." />
349 </options>
350 </param>
351 </when>
352 <when value="history">
353 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
354 </when>
355 </conditional>
356 </xml>
357
358 <token name="@reference_genome_source@">
359 #if $source.ref_source=="history":
360 --genome $source.input1
361 #else:
362 --genome "$source.input1_2bit.fields.path"
363 #end if
364 </token>
365
366 <xml name="effectiveGenomeSize">
367 <conditional name="effectiveGenomeSize">
368 <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
369 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.
370 Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly.
371 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.">
372 <option value="93260000">ce10 (93260000)</option>
373 <option value="121400000">dm3 (121400000)</option>
374 <option value="2451960000" selected="true">hg19 (2451960000)</option>
375 <option value="2150570000">mm9 (2150570000)</option>
376 <option value="specific">user specified</option>
377 </param>
378 <when value="specific">
379 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
380 </when>
381 <when value="2150570000" />
382 <when value="2451960000" />
383 <when value="121400000" />
384 <when value="93260000" />
385 </conditional>
386 </xml>
387
388 <xml name="skipNAs">
389 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
390 label="Ignore missing data?"
391 help="This parameter determines if non-covered regions
392 (regions without overlapping reads) in a bam/bigWig file
393 should be skipped. The default is to treat those
394 regions as having a value of zero. The decision to
395 skip non-covered regions depends on the interpretation
396 of the data. Non-covered regions may represent, for
397 example, repetitive regions that should be ignored.
398 (default: False)" />
399 </xml>
400
401 <xml name="input_save_matrix_values">
402 <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
403 </xml>
404
405 <xml name="input_graphic_output_settings">
406 <conditional name="output" >
407 <param name="showOutputSettings" type="select" label="Show advanced output settings" >
408 <option value="no" selected="true">no</option>
409 <option value="yes">yes</option>
410 </param>
411 <when value="no" />
412 <when value="yes">
413 <yield />
414 <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."/>
415 </when>
416 </conditional>
417 </xml>
418
419
420 <xml name="input_image_file_format">
421 <param argument="--outFileFormat" type="select" label="Image file format">
422 <option value="png" selected="true">png</option>
423 <option value="pdf">pdf</option>
424 <option value="svg">svg</option>
425 <option value="eps">eps</option>
426 </param>
427 </xml>
428
429 <xml name="output_image_file_format">
430 <data format="png" name="outFileName" label="${tool.name} image">
431 <change_format>
432 <when input="output.outFileFormat" value="pdf" format="pdf" />
433 <when input="output.outFileFormat" value="svg" format="svg" />
434 <when input="output.outFileFormat" value="eps" format="eps" />
435 </change_format>
436 </data>
437 </xml>
438
439 <xml name="output_image_file_format_not_nested">
440 <data format="png" name="outFileName" label="${tool.name} image">
441 <change_format>
442 <when input="outFileFormat" value="pdf" format="pdf" />
443 <when input="outFileFormat" value="svg" format="svg" />
444 <when input="outFileFormat" value="eps" format="eps" />
445 </change_format>
446 </data>
447 </xml>
448
449 <xml name="output_save_matrix_values">
450 <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
451 <filter>
452 ((
453 output['showOutputSettings'] == 'yes' and
454 output['saveMatrix'] is True
455 ))
456 </filter>
457 </data>
458 </xml>
459
460 <xml name="output_graphic_outputs">
461 <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
462 <filter>
463 ((
464 output['showOutputSettings'] == 'yes' and
465 output['saveSortedRegions'] is True
466 ))
467 </filter>
468 </data>
469 </xml>
470
471 <xml name="colorMap">
472 <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/">
473 <option value="RdYlBu" selected="true">RdYlBu</option>
474 <option value="Accent">Accent</option>
475 <option value="Spectral">Spectral</option>
476 <option value="Set1">Set1</option>
477 <option value="Set2">Set2</option>
478 <option value="Set3">Set3</option>
479 <option value="Dark2">Dark2</option>
480 <option value="Reds">Reds</option>
481 <option value="Oranges">Oranges</option>
482 <option value="Greens">Greens</option>
483 <option value="Blues">Blues</option>
484 <option value="Greys">Greys</option>
485 <option value="Purples">Purples</option>
486 <option value="Paired">Paired</option>
487 <option value="Pastel1">Pastel1</option>
488 <option value="Pastel2">Pastel2</option>
489 <option value="spring">spring</option>
490 <option value="summer">summer</option>
491 <option value="autumn">autumn</option>
492 <option value="winter">winter</option>
493 <option value="hot">hot</option>
494 <option value="coolwarm">coolwarm</option>
495 <option value="cool">cool</option>
496 <option value="seismic">seismic</option>
497 <option value="terrain">terrain</option>
498 <option value="ocean">ocean</option>
499 <option value="rainbow">rainbow</option>
500 <option value="bone">bone</option>
501 <option value="flag">flag</option>
502 <option value="prism">prism</option>
503 <option value="cubehelix">cubehelix</option>
504 <option value="binary">binary</option>
505 <option value="pink">pink</option>
506 <option value="gray">gray</option>
507 <option value="copper">copper</option>
508 <option value="BrBG">BrBG</option>
509 <option value="BuGn">BuGn</option>
510 <option value="BuPu">BuPu</option>
511 <option value="GnBu">GnBu</option>
512 <option value="OrRd">OrRd</option>
513 <option value="PiYG">PiYG</option>
514 <option value="PRGn">PRGn</option>
515 <option value="PuOr">PuOr</option>
516 <option value="PuRd">PuRd</option>
517 <option value="PuBu">PuBu</option>
518 <option value="RdBu">RdBu</option>
519 <option value="RdGy">RdGy</option>
520 <option value="RdPu">RdPu</option>
521 <option value="YlGn">YlGn</option>
522 <option value="PuBuGn">PuBuGn</option>
523 <option value="RdYlGn">RdYlGn</option>
524 <option value="YlGnBu">YlGnBu</option>
525 <option value="YlOrBr">YlOrBr</option>
526 <option value="YlOrRd">YlOrRd</option>
527 <option value="gist_gray">gist_gray</option>
528 <option value="gist_stern">gist_stern</option>
529 <option value="gist_earth">gist_earth</option>
530 <option value="gist_yarg">gist_yarg</option>
531 <option value="gist_ncar">gist_ncar</option>
532 <option value="gist_rainbow">gist_rainbow</option>
533 <option value="gist_heat">gist_heat</option>
534 <option value="gnuplot">gnuplot</option>
535 <option value="gnuplot2">gnuplot2</option>
536 <option value="CMRmap">CMRmap</option>
537 <option value="bwr">bwr</option>
538 <option value="hsv">hsv</option>
539 <option value="brg">brg</option>
540 <option value="jet">jet</option>
541 <option value="afmhot">afmhot</option>
542 <option value="Accent_r">Accent reversed</option>
543 <option value="Spectral_r">Spectral reversed</option>
544 <option value="Set1_r">Set1 reversed</option>
545 <option value="Set2_r">Set2 reversed</option>
546 <option value="Set3_r">Set3 reversed</option>
547 <option value="Dark2_r">Dark2 reversed</option>
548 <option value="Reds_r">Reds reversed</option>
549 <option value="Oranges_r">Oranges reversed</option>
550 <option value="Greens_r">Greens reversed</option>
551 <option value="Blues_r">Blues reversed</option>
552 <option value="Greys_r">Greys reversed</option>
553 <option value="Purples_r">Purples reversed</option>
554 <option value="Paired_r">Paired reversed</option>
555 <option value="Pastel1_r">Pastel1 reversed</option>
556 <option value="Pastel2_r">Pastel2 reversed</option>
557 <option value="spring_r">spring reversed</option>
558 <option value="summer_r">summer reversed</option>
559 <option value="autumn_r">autumn reversed</option>
560 <option value="winter_r">winter reversed</option>
561 <option value="hot_r">hot reversed</option>
562 <option value="coolwarm_r">coolwarm reversed</option>
563 <option value="cool_r">cool reversed</option>
564 <option value="seismic_r">seismic reversed</option>
565 <option value="terrain_r">terrain reversed</option>
566 <option value="ocean_r">ocean reversed</option>
567 <option value="rainbow_r">rainbow reversed</option>
568 <option value="bone_r">bone reversed</option>
569 <option value="flag_r">flag reversed</option>
570 <option value="prism_r">prism reversed</option>
571 <option value="cubehelix_r">cubehelix reversed</option>
572 <option value="binary_r">binary reversed</option>
573 <option value="pink_r">pink reversed</option>
574 <option value="gray_r">gray reversed</option>
575 <option value="copper_r">copper reversed</option>
576 <option value="BrBG_r">BrBG reversed</option>
577 <option value="BuGn_r">BuGn reversed</option>
578 <option value="BuPu_r">BuPu reversed</option>
579 <option value="GnBu_r">GnBu reversed</option>
580 <option value="OrRd_r">OrRd reversed</option>
581 <option value="PiYG_r">PiYG reversed</option>
582 <option value="PRGn_r">PRGn reversed</option>
583 <option value="PuOr_r">PuOr reversed</option>
584 <option value="PuRd_r">PuRd reversed</option>
585 <option value="PuBu_r">PuBu reversed</option>
586 <option value="RdBu_r">RdBu reversed</option>
587 <option value="RdGy_r">RdGy reversed</option>
588 <option value="RdPu_r">RdPu reversed</option>
589 <option value="YlGn_r">YlGn reversed</option>
590 <option value="PuBuGn_r">PuBuGn reversed</option>
591 <option value="RdYlBu_r">RdYlBu reversed</option>
592 <option value="RdYlGn_r">RdYlGn reversed</option>
593 <option value="YlGnBu_r">YlGnBu reversed</option>
594 <option value="YlOrBr_r">YlOrBr reversed</option>
595 <option value="YlOrRd_r">YlOrRd reversed</option>
596 <option value="gist_gray_r">gist_gray reversed</option>
597 <option value="gist_stern_r">gist_stern reversed</option>
598 <option value="gist_earth_r">gist_earth reversed</option>
599 <option value="gist_yarg_r">gist_yarg reversed</option>
600 <option value="gist_ncar_r">gist_ncar reversed</option>
601 <option value="gist_rainbow_r">gist_rainbow reversed</option>
602 <option value="gist_heat_r">gist_heat reversed</option>
603 <option value="gnuplot_r">gnuplot reversed</option>
604 <option value="gnuplot2_r">gnuplot2 reversed</option>
605 <option value="CMRmap_r">CMRmap reversed</option>
606 <option value="bwr_r">bwr reversed</option>
607 <option value="hsv_r">hsv reversed</option>
608 <option value="brg_r">brg reversed</option>
609 <option value="jet_r">jet reversed</option>
610 <option value="afmhot_r">afmhot reversed</option>
611 </param>
612
613 </xml>
614
615 </macros>