Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

comparison deepTools_macros.xml @ 8:dc8d6e07d829 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe
author bgruening
date Mon, 19 Sep 2016 17:25:47 -0400
parents b4886e1369c4
children 4efe24a9739e
comparison
equal deleted inserted replaced
7:b4886e1369c4 8:dc8d6e07d829
28 --samFlagInclude $advancedOpt.samFlagInclude 28 --samFlagInclude $advancedOpt.samFlagInclude
29 #end if 29 #end if
30 #if $advancedOpt.samFlagExclude: 30 #if $advancedOpt.samFlagExclude:
31 --samFlagExclude $advancedOpt.samFlagExclude 31 --samFlagExclude $advancedOpt.samFlagExclude
32 #end if 32 #end if
33 #if $advancedOpt.minFragmentLength:
34 --minFragmentLength $advancedOpt.minFragmentLength
35 #end if
36 #if $advancedOpt.maxFragmentLength:
37 --maxFragmentLength $advancedOpt.maxFragmentLength
38 #end if
39 </token>
40
41 <token name="@ADVANCED_OPTS_GTF@">
42 $advancedOpt.metagene
43 #if $advancedOpt.transcriptID:
44 --transcriptID $advancedOpt.transcriptID
45 #end if
46 #if $advancedOpt.exonID:
47 --exonID $advancedOpt.exonID
48 #end if
49 #if $advancedOpt.transcript_id_designator:
50 --transcript_id_designator $advancedOpt.transcript_id_designator
51 #end if
33 </token> 52 </token>
34 53
35 <xml name="heatmap_options"> 54 <xml name="heatmap_options">
36 <expand macro="zMin_zMax" /> 55 <expand macro="zMin_zMax" />
37 <expand macro="colorMap" /> 56 <expand macro="colorMap" />
57 label="Include zeros" 76 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." /> 77 help="If set, then regions with zero counts for *all* BAM files are included. The default behavior is to ignore such regions." />
59 </xml> 78 </xml>
60 79
61 <xml name="zMin_zMax"> 80 <xml name="zMin_zMax">
62 <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities" 81 <param argument="--zMin" type="text" value="" optional="true" label="Minimum value for the heatmap intensities"
63 help="If not specified the value is set automatically."/> 82 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" 83 <param argument="--zMax" type="text" value="" optional="true" label="Maximum value for the heatmap intensities"
65 help="If not specified the value is set automatically."/> 84 help="If not specified the value is set automatically."/>
66 </xml> 85 </xml>
67 86
68 <xml name="region_limit_operation"> 87 <xml name="region_limit_operation">
69 <param argument="--region" type="text" value="" 88 <param argument="--region" type="text" value=""
70 label="Region of the genome to limit the operation to" 89 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;."> 90 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 <sanitizer> 91 <sanitizer>
73 <valid initial="string.letters,string.digits"> 92 <valid initial="string.letters,string.digits">
74 <add value="|"/> 93 <add value="|"/>
94 <add value=":"/>
75 </valid> 95 </valid>
76 </sanitizer> 96 </sanitizer>
77 </param> 97 </param>
78 </xml> 98 </xml>
79 99
80 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> 100 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
81 <token name="@WRAPPER_VERSION@">2.2.3</token> 101 <token name="@WRAPPER_VERSION@">2.3.5</token>
82 <xml name="requirements"> 102 <xml name="requirements">
83 <requirements> 103 <requirements>
84 <requirement type="package" version="2.7.10">python</requirement> 104 <requirement type="package" version="2.7.10">python</requirement>
85 <requirement type="binary">@BINARY@</requirement> 105 <requirement type="package" version="2.3.5">deepTools</requirement>
86 <requirement type="package" version="2.2.3">deepTools</requirement>
87 <yield /> 106 <yield />
88 </requirements> 107 </requirements>
89 <expand macro="stdio" /> 108 <expand macro="stdio" />
90 <version_command>@BINARY@ --version</version_command> 109 <version_command>@BINARY@ --version</version_command>
91 </xml> 110 </xml>
157 <param argument="--samFlagExclude" type="integer" optional="True" value="" 176 <param argument="--samFlagExclude" type="integer" optional="True" value=""
158 label="Exclude reads based on the SAM flag" 177 label="Exclude reads based on the SAM flag"
159 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."/> 178 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."/>
160 </xml> 179 </xml>
161 180
181 <xml name="fragLength">
182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
183 label="Minimum fragment length for inclusion."
184 help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
186 label="Maximum fragment length for inclusion."
187 help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
188 </xml>
189
162 <xml name="read_processing_options"> 190 <xml name="read_processing_options">
163 <expand macro="extendReads" /> 191 <expand macro="extendReads" />
164 <expand macro="ignoreDuplicates" /> 192 <expand macro="ignoreDuplicates" />
165 <expand macro="centerReads" /> 193 <expand macro="centerReads" />
166 <expand macro="minMappingQuality" /> 194 <expand macro="minMappingQuality" />
167 <expand macro="samFlags" /> 195 <expand macro="samFlags" />
168 </xml> 196 <expand macro="fragLength" />
197 </xml>
198
199 <xml name="gtf_options">
200 <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
201 label="Use a metagene model"
202 help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
203 <param argument="--transcriptID" optional="True" value="transcript" type="text"
204 label="trascript designator"
205 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
206 <param argument="--exonID" optional="True" value="exon" type="text"
207 label="exon designator"
208 help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as exons. CDS would be another common value for this. Default: exon" />
209 <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"
210 label="transcriptID key designator"
211 help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
212 or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
213 as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
214 convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
215 </xml>
216
169 217
170 <xml name="plotNumbers"> 218 <xml name="plotNumbers">
171 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" 219 <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
172 label="Plot the correlation value" 220 label="Plot the correlation value"
173 help="If set, then the correlation number is plotted on top of the heatmap."/> 221 help="If set, then the correlation number is plotted on top of the heatmap."/>
245 <option value="ascend">ascending order</option> 293 <option value="ascend">ascending order</option>
246 </param> 294 </param>
247 </xml> 295 </xml>
248 296
249 <xml name="minMappingQuality"> 297 <xml name="minMappingQuality">
250 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1" 298 <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="0"
251 label="Minimum mapping quality" 299 label="Minimum mapping quality"
252 help= "If set, only reads with a mapping quality score higher than this value are considered."/> 300 help= "If set, only reads with a mapping quality score higher than this value are considered."/>
253 </xml> 301 </xml>
254 302
255 <xml name="skipZeros"> 303 <xml name="skipZeros">
359 ln -s "${bigwig}" "${counter}.bw" && 407 ln -s "${bigwig}" "${counter}.bw" &&
360 #silent $files.append('%s.bw' % $counter) 408 #silent $files.append('%s.bw' % $counter)
361 #silent $labels.append("'%s'" % ($bigwig.display_name)) 409 #silent $labels.append("'%s'" % ($bigwig.display_name))
362 #end for 410 #end for
363 ]]> 411 ]]>
412 </token>
413
414 <xml name="blacklist">
415 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
416 label="Blacklisted regions in BED/GTF format"
417 help="One or more files containing regions to exclude from the analysis" />
418 </xml>
419
420 <token name="@blacklist@">
421 <![CDATA[
422 #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
423 #set blfiles=[]
424 #for $f in $advancedOpt.blackListFileName:
425 #silent $blfiles.append("'%s'" % $f)
426 #end for
427 #if $blfiles != ["'None'"]:
428 --blackListFileName #echo ' '.join($blfiles)#
429 #end if
430 #end if
431 ]]>
432 </token>
433
434 <xml name="multiple_bed">
435 <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
436 label="Regions in BED/GTF format"
437 help="One or more files containing regions to include in the analysis" />
438 </xml>
439
440 <token name="@multiple_bed@">
441 <![CDATA[
442 #set files=[]
443 #set labels=[]
444 #for $f in $BED:
445 #silent $files.append("'%s'" % $f)
446 #silent $labels.append("'%s'" % $f.display_name)
447 #end for
448 #if len($files) > 0:
449 --BED #echo ' '.join($files)#
450 --regionLabels #echo ' '.join($labels)#
451 #end if
452 ]]>
364 </token> 453 </token>
365 454
366 <xml name="reference_genome_source"> 455 <xml name="reference_genome_source">
367 <conditional name="source"> 456 <conditional name="source">
368 <param name="ref_source" type="select" label="Reference genome"> 457 <param name="ref_source" type="select" label="Reference genome">
402 <option value="2451960000" selected="true">hg19 (2451960000)</option> 491 <option value="2451960000" selected="true">hg19 (2451960000)</option>
403 <option value="2150570000">mm9 (2150570000)</option> 492 <option value="2150570000">mm9 (2150570000)</option>
404 <option value="specific">user specified</option> 493 <option value="specific">user specified</option>
405 </param> 494 </param>
406 <when value="specific"> 495 <when value="specific">
407 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/> 496 <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size"
497 help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
408 </when> 498 </when>
409 <when value="2150570000" /> 499 <when value="2150570000" />
410 <when value="2451960000" /> 500 <when value="2451960000" />
411 <when value="121400000" /> 501 <when value="121400000" />
412 <when value="93260000" /> 502 <when value="93260000" />
437 <option value="yes">yes</option> 527 <option value="yes">yes</option>
438 </param> 528 </param>
439 <when value="no" /> 529 <when value="no" />
440 <when value="yes"> 530 <when value="yes">
441 <yield /> 531 <yield />
442 <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."/> 532 <param name="saveSortedRegions" type="boolean"
533 label="Save the regions after skipping zeros or min/max threshold values"
534 help="The order of the regions in the file follows the sorting order selected. This is useful,
535 for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
443 </when> 536 </when>
444 </conditional> 537 </conditional>
445 </xml> 538 </xml>
446 539
447 540
450 <option value="png" selected="true">png</option> 543 <option value="png" selected="true">png</option>
451 <option value="pdf">pdf</option> 544 <option value="pdf">pdf</option>
452 <option value="svg">svg</option> 545 <option value="svg">svg</option>
453 <option value="eps">eps</option> 546 <option value="eps">eps</option>
454 </param> 547 </param>
548 </xml>
549
550 <xml name="output_dpi">
551 <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
552 label="Image dpi" help=""/>
455 </xml> 553 </xml>
456 554
457 <xml name="output_image_file_format"> 555 <xml name="output_image_file_format">
458 <data format="png" name="outFileName" label="${tool.name} image"> 556 <data format="png" name="outFileName" label="${tool.name} image">
459 <change_format> 557 <change_format>
495 </filter> 593 </filter>
496 </data> 594 </data>
497 </xml> 595 </xml>
498 596
499 <xml name="colorMap"> 597 <xml name="colorMap">
500 <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"> 598 <param name="colorMap" type="select" label="Color map to use for the heatmap"
599 help=" Available color map names can be found here: http://matplotlib.org/examples/color/colormaps_reference.html"
600 multiple="true">
501 <option value="RdYlBu" selected="true">RdYlBu</option> 601 <option value="RdYlBu" selected="true">RdYlBu</option>
502 <option value="Accent">Accent</option> 602 <option value="Accent">Accent</option>
503 <option value="Spectral">Spectral</option> 603 <option value="Spectral">Spectral</option>
504 <option value="Set1">Set1</option> 604 <option value="Set1">Set1</option>
505 <option value="Set2">Set2</option> 605 <option value="Set2">Set2</option>