Mercurial > repos > bgruening > deeptools_compute_matrix

comparison deepTools_macros.xml @ 3:2f2dd609644f draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f
author bgruening
date Mon, 21 Dec 2015 07:25:28 -0500
parents fb65748c2594
children 28b07293f1ab
comparison
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2:fb65748c2594 3:2f2dd609644f
12 </when> 12 </when>
13 </conditional> 13 </conditional>
14 </xml> 14 </xml>
15 15
16 <token name="@ADVANCED_OPTS_READ_PROCESSING@"> 16 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
17 --extendReads $advancedOpt.extendReads 17 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
18 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
19 #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
20 --extendReads
21 #end if
18 $advancedOpt.ignoreDuplicates 22 $advancedOpt.ignoreDuplicates
19 $advancedOpt.centerReads 23 $advancedOpt.centerReads
20 #if $advancedOpt.minMappingQuality: 24 #if $advancedOpt.minMappingQuality:
21 --minMappingQuality '$advancedOpt.minMappingQuality' 25 --minMappingQuality '$advancedOpt.minMappingQuality'
22 #end if 26 #end if
34 <expand macro="plotTitle" /> 38 <expand macro="plotTitle" />
35 <expand macro="plotNumbers" /> 39 <expand macro="plotNumbers" />
36 </xml> 40 </xml>
37 41
38 <token name="@HEATMAP_OPTIONS@"> 42 <token name="@HEATMAP_OPTIONS@">
39 #if $zMin: 43 #if $plotting_type.zMin:
40 --zMin $zMin 44 --zMin $plotting_type.zMin
41 #end if 45 #end if
42 #if $zMax: 46 #if $plotting_type.zMax:
43 --zMax $zMax 47 --zMax $plotting_type.zMax
44 #end if 48 #end if
45 --colorMap '$colorMap' 49 --colorMap '$plotting_type.colorMap'
46 $plotNumbers 50 $plotting_type.plotNumbers
47 --plotTitle $plotTitle 51 --plotTitle '$plotting_type.plotTitle'
48 </token> 52 </token>
49 53
50 54
51 <xml name="includeZeros"> 55 <xml name="includeZeros">
52 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue="" 56 <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
53 label="Include zeros" 57 label="Include zeros"
54 help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." /> 58 help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
55 </xml> 59 </xml>
56 60
57 <xml name="zMin_zMax"> 61 <xml name="zMin_zMax">
58 <param argument="--zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities" 62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
59 help="If not specified the value is set automatically."/> 63 help="If not specified the value is set automatically."/>
60 <param argument="--zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities" 64 <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
61 help="If not specified the value is set automatically."/> 65 help="If not specified the value is set automatically."/>
62 </xml> 66 </xml>
63 67
64 <xml name="region_limit_operation"> 68 <xml name="region_limit_operation">
65 <param argument="--region" type="text" value="" 69 <param argument="--region" type="text" value=""
144 label="Plot the correlation value" 148 label="Plot the correlation value"
145 help="If set, then the correlation number is plotted on top of the heatmap."/> 149 help="If set, then the correlation number is plotted on top of the heatmap."/>
146 </xml> 150 </xml>
147 151
148 <xml name="extendReads"> 152 <xml name="extendReads">
149 <param argument="--extendReads" type="integer" value="" optional="True" 153 <conditional name="doExtendCustom">
150 label="Extend reads to the given average fragment size" 154 <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
151 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. 155 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.
152 By default *each* read mate is extended. 156 By default *each* read mate is extended.
153 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate. 157 This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
154 Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value. 158 Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value.
155 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 159 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
156 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."/> 160 recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
161 <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
162 <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
163 <option value="custom">A custom length, which will be applied to ALL reads.</option>
164 </param>
165 <when value="no" />
166 <when value="yes" />
167 <when value="custom">
168 <param name="extendReadsValue" type="integer" value="300" min="1"
169 label="Extend reads to the given average fragment size"
170 help="Extend all reads to this length" />
171 </when>
172 </conditional>
157 </xml> 173 </xml>
158 174
159 <xml name="corMethod"> 175 <xml name="corMethod">
160 <param argument="--corMethod" type="select" label="Correlation method"> 176 <param argument="--corMethod" type="select" label="Correlation method">
161 <option value="spearman" selected="True">Spearman</option> 177 <option value="spearman" selected="True">Spearman</option>
272 <yield /> 288 <yield />
273 </citations> 289 </citations>
274 </xml> 290 </xml>
275 291
276 <xml name="multiple_input_bams"> 292 <xml name="multiple_input_bams">
277 <param argument="--bamfiles" type="data" format="bam" 293 <param argument="--bamfiles" type="data" format="bam" min="2"
278 label="Bam file" multiple="true" 294 label="Bam file" multiple="true"
279 help="The BAM file must be sorted."/> 295 help="The BAM file must be sorted."/>
280 </xml> 296 </xml>
281 297
282 <xml name="multiple_input_bigwigs"> 298 <xml name="multiple_input_bigwigs">
283 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" 299 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
284 label="Bigwig file" 300 label="Bigwig file"
285 help="The Bigwig file must be sorted."/> 301 help="The Bigwig file must be sorted."/>
286 </xml> 302 </xml>
287 303
288 <xml name="plotTitle"> 304 <xml name="plotTitle">
364 <when value="121400000" /> 380 <when value="121400000" />
365 <when value="93260000" /> 381 <when value="93260000" />
366 </conditional> 382 </conditional>
367 </xml> 383 </xml>
368 384
369 <xml name="image_file_format">
370 <param argument="--outFileFormat" type="select" label="Image file format">
371 <option value="png" selected="true">png</option>
372 <option value="pdf">pdf</option>
373 <option value="svg">svg</option>
374 <option value="eps">eps</option>
375 </param>
376 </xml>
377
378 <xml name="skipNAs"> 385 <xml name="skipNAs">
379 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False" 386 <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
380 label="Ignore missing data?" 387 label="Ignore missing data?"
381 help="This parameter determines if non-covered regions 388 help="This parameter determines if non-covered regions
382 (regions without overlapping reads) in a bam/bigWig file 389 (regions without overlapping reads) in a bam/bigWig file
405 <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."/> 412 <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."/>
406 </when> 413 </when>
407 </conditional> 414 </conditional>
408 </xml> 415 </xml>
409 416
417
410 <xml name="input_image_file_format"> 418 <xml name="input_image_file_format">
411 <param name="outFileFormat" type="select" label="Image file format"> 419 <param argument="--outFileFormat" type="select" label="Image file format">
412 <option value="png" selected="true">png</option> 420 <option value="png" selected="true">png</option>
413 <option value="pdf">pdf</option> 421 <option value="pdf">pdf</option>
414 <option value="svg">svg</option> 422 <option value="svg">svg</option>
415 <option value="eps">eps</option> 423 <option value="eps">eps</option>
416 <option value="emf">emf</option>
417 </param> 424 </param>
418 </xml> 425 </xml>
419 426
420 <xml name="output_image_file_format"> 427 <xml name="output_image_file_format">
421 <data format="png" name="outFileName" label="${tool.name} image"> 428 <data format="png" name="outFileName" label="${tool.name} image">
422 <change_format> 429 <change_format>
423 <when input="output.outFileFormat" value="pdf" format="pdf" /> 430 <when input="output.outFileFormat" value="pdf" format="pdf" />
424 <when input="output.outFileFormat" value="svg" format="svg" /> 431 <when input="output.outFileFormat" value="svg" format="svg" />
425 <when input="output.outFileFormat" value="eps" format="eps" /> 432 <when input="output.outFileFormat" value="eps" format="eps" />
426 <when input="output.outFileFormat" value="emf" format="emf" /> 433 </change_format>
434 </data>
435 </xml>
436
437 <xml name="output_image_file_format_not_nested">
438 <data format="png" name="outFileName" label="${tool.name} image">
439 <change_format>
440 <when input="outFileFormat" value="pdf" format="pdf" />
441 <when input="outFileFormat" value="svg" format="svg" />
442 <when input="outFileFormat" value="eps" format="eps" />
427 </change_format> 443 </change_format>
428 </data> 444 </data>
429 </xml> 445 </xml>
430 446
431 <xml name="output_save_matrix_values"> 447 <xml name="output_save_matrix_values">