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1 <tool id="multigps" name="MultiGPS" version="0.74.0">
2 <description>analyzes collections of multi-condition ChIP-seq data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="0.74">multigps</requirement>
8 </requirements>
9 <command detect_errors="aggressive">
10 <![CDATA[
11 #set output_dir = $output_html.files_path
12 mkdir -p $output_dir &&
13 multigps
14 ## General options
15 --design '$build_design_file'
16 ## Append .txt extensions to events hrefs
17 ## in output dataset so files will render
18 ## in the browser.
19 --eventsaretxt
20 ## Do not run the parallel version of meme.
21 --meme1proc
22 --threads \${GALAXY_SLOTS:-4}
23 --geninfo '$chromInfo'
24 ## Advanced options
25 #set aoc = $advanced_options_cond
26 #if str($aoc.advanced_options) == 'display':
27 #set bmsc = $aoc.binding_model_smoothing_cond
28 #set gmsc = $aoc.gauss_model_smoothing_cond
29 #set rbec = $aoc.report_binding_events_cond
30 #set rloc = $aoc.reads_limits_options_cond
31 #set sdc = $aoc.scale_data_cond
32 #set umc = $aoc.use_motif_cond
33 #if str($umc.use_motif) == 'yes':
34 #set rgc = $umc.reference_genome_cond
35 --seq
36 #if str($rgc.reference_genome_source) == 'cached':
37 '${rgc.reference_genome.fields.path}'
38 #else:
39 '${rgc.reference_genome}'
40 #end if
41 #end if
42 ## Limits on how many reads
43 #if str($rloc.reads_limits) == 'yes':
44 --fixedpb $rloc.fixedpb
45 --poissongausspb $rloc.poissongausspb
46 #if str($rloc.nonunique) == 'yes':
47 --nonunique
48 #end if
49 --mappability $rloc.mappability
50 #if str($rloc.nocache) == 'yes':
51 --nocache
52 #end if
53 #end if
54 ## Scaling data
55 #if str($sdc.scale_data) == 'yes':
56 #if str($sdc.scaling) == 'no':
57 --noscaling $sdc.scaling
58 #end if
59 #if str($sdc.medianscale) == 'yes':
60 --medianscale $sdc.medianscale
61 #end if
62 #if str($sdc.regressionscale) == 'yes':
63 --regressionscale $sdc.regressionscale
64 #end if
65 #if str($sdc.sesscale) == 'yes':
66 --sesscale $sdc.sesscale
67 #end if
68 #if $sdc.fixedscaling > 0:
69 ‒‒fixedscaling $sdc.fixedscaling
70 #end if
71 --scalewin $sdc.scalewin
72 #if str($sdc.plotscaling) == 'yes':
73 --plotscaling $sdc.plotscaling
74 #end if
75 #end if
76 ## Running MultiGPS
77 #if str($aoc.readdistributionfile) != 'None':
78 --readdistributionfile '$aoc.readdistributionfile'
79 #end if
80 --maxtrainingrounds $aoc.maxtrainingrounds
81 #if str($aoc.nomodelupdate) == 'no':
82 --nomodelupdate
83 #end if
84 --minmodelupdateevents $aoc.minmodelupdateevents
85 #if str($bmsc.nomodelsmoothing) == 'no':
86 --nomodelsmoothing
87 #else:
88 --splinesmoothparam $bmsc.splinesmoothparam
89 #end if
90 #if str($gmsc.gaussmodelsmoothing) == 'yes':
91 --gaussmodelsmoothing
92 --gausssmoothparam $gmsc.gausssmoothparam
93 #end if
94 #if str($aoc.jointinmodel) == 'yes':
95 --jointinmodel
96 #end if
97 #if str($aoc.fixedmodelrange) == 'yes':
98 --fixedmodelrange
99 #end if
100 --prlogconf $aoc.prlogconf
101 #if $aoc.fixedalpha > 0:
102 --fixedalpha $aoc.fixedalpha
103 #end if
104 --alphascale $aoc.alphascale
105 #if str($aoc.mlconfignotshared) == 'no':
106 --mlconfignotshared
107 #end if
108 #if str($aoc.exclude) != 'None':
109 --exclude '$aoc.exclude'
110 #end if
111 ## MultiGPS priors
112 #if str($umc.use_motif) == 'yes':
113 #set mpc = $umc.multigps_priors_cond
114 #if str($mpc.multigps_priors) == 'yes':
115 #set bmc = $mpc.both_motifs_cond
116 #if str($mpc.noposprior) == 'no':
117 --noposprior
118 #end if
119 --probshared $mpc.probshared
120 #if str($bmc.nomotifs) == 'yes':
121 --memenmotifs $bmc.memenmotifs
122 --mememinw $bmc.mememinw
123 --mememaxw $bmc.mememaxw
124 #else:
125 #set nmpc = $bmc.nomotifprior_cond
126 --nomotifs
127 #if str($nmpc.nomotifprior) == 'yes':
128 --nomotifprior
129 --memenmotifs $nmpc.memenmotifs
130 --mememinw $nmpc.mememinw
131 --mememaxw $nmpc.mememaxw
132 #end if
133 #end if
134 #end if
135 #end if
136 ## Reporting binding events
137 #if str($rbec.report_binding_events) == 'yes':
138 --minqvalue $rbec.minqvalue
139 --minfold $rbec.minfold
140 #if str($rbec.nodifftests) == 'no':
141 --nodifftests
142 #end if
143 --edgerod $rbec.edgerod
144 --diffp $rbec.diffp
145 #end if
146 #end if
147 2>&1
148 --out '$output_html.files_path'
149 #if str($save_design_file) == 'yes':
150 && cp '$build_design_file' '$output_design_file'
151 #end if
152 && mv $output_dir/*.counts '$replicates_counts'
153 && mv $output_dir/*.bed '$output_bed'
154 && mv $output_dir/*.html '$output_html'
155 && mv $output_dir/*.table.txt '$all_events_table'
156 ]]>
157 </command>
158 <configfiles>
159 <configfile name="build_design_file"><![CDATA[#for $condition_items in $condition_repeat:
160 #for $signal_items in $condition_items.signal_repeat:
161 #if str($signal_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
162 #set $frc = $signal_items.fixedreadcount_cond.fixedreadcount
163 #else:
164 #set $frc = ''
165 #end if
166 ${signal_items.signal} Signal ${signal_items.signal.ext.upper()} ${condition_items.condition_name} ${signal_items.replicate_name} ${condition_items.experiment_type} ${frc}
167 #end for
168 #for $control_items in $condition_items.control_repeat:
169 #if str($control_items.specify_replicate_name_cond.specify_replicate_name) == 'yes':
170 #set $rn = $control_items.specify_replicate_name_cond.replicate_name
171 #else:
172 #set $rn = ''
173 #end if
174 #if str($control_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
175 #set $frc = $control_items.fixedreadcount_cond.fixedreadcount
176 #else:
177 #set $frc = ''
178 #end if
179 ${control_items.control} Control ${control_items.control.ext.upper()} ${condition_items.condition_name} ${rn} ${condition_items.experiment_type} ${frc}
180 #end for
181 #end for ]]></configfile>
182 </configfiles>
183 <inputs>
184 <repeat name="condition_repeat" title="Condition" min="1">
185 <param name="condition_name" type="text" value="cond" label="Condition name">
186 <validator type="empty_field" />
187 </param>
188 <expand macro="param_experiment_type" />
189 <repeat name="signal_repeat" title="Signal" min="1">
190 <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
191 <validator type="unspecified_build" />
192 </param>
193 <param name="replicate_name" type="text" value="1" label="Replicate name">
194 <validator type="empty_field" />
195 </param>
196 <expand macro="cond_fixedreadcount" />
197 </repeat>
198 <repeat name="control_repeat" title="Control" min="0">
199 <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx">
200 <validator type="unspecified_build" />
201 </param>
202 <conditional name="specify_replicate_name_cond">
203 <param name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control. If used, the control will only be used for the corresponding named signal replicate">
204 <option value="no" selected="True">No</option>
205 <option value="yes">Yes</option>
206 </param>
207 <when value="yes">
208 <param name="replicate_name" type="text" optional="true" label="Replicate name"/>
209 </when>
210 <when value="no" />
211 </conditional>
212 <expand macro="cond_fixedreadcount" />
213 </repeat>
214 </repeat>
215 <param name="save_design_file" type="select" display="radio" label="Output design file?">
216 <option value="no" selected="true">No</option>
217 <option value="yes">Yes</option>
218 </param>
219 <!-- Advanced options -->
220 <conditional name="advanced_options_cond">
221 <param name="advanced_options" type="select" label="Advanced options">
222 <option value="hide" selected="true">Hide</option>
223 <option value="display">Display</option>
224 </param>
225 <when value="display">
226 <!-- Limits on how many reads -->
227 <conditional name="reads_limits_options_cond">
228 <param name="reads_limits" type="select" label="Set limits on how many reads can have their 5′ end at the same position in each replicate?" help="Default behavior is to estimate a global per-base limit from a Poisson distribution parameterized by the number of reads divided by the number of mappable bases in the genome. The per-base limit is set as the count corresponding to the 10^-7 probability level from the Poisson.">
229 <option value="no" selected="True">No</option>
230 <option value="yes">Yes</option>
231 </param>
232 <when value="no" />
233 <when value="yes">
234 <param name="fixedpb" type="integer" value="0" min="0" label="Fixed per-base limit" help="Zero value estimates from background model"/>
235 <param name="poissongausspb" type="integer" value="0" min="0" label="Poisson threshold for filtering per base" help="Filter per base using the specified Poisson threshold parameterized by a local Gaussian sliding window" />
236 <param name="nonunique" type="select" label="Use non-unique reads?">
237 <option value="no" selected="True">No</option>
238 <option value="yes">Yes</option>
239 </param>
240 <param name="mappability" type="float" value="0.0" min="0.8" label="Fraction of the genome that is mappable for these experiments" />
241 <param name="nocache" type="select" label="Turn off caching of the entire set of experiments?" help="Run slower with less memory" >
242 <option value="no" selected="True">No</option>
243 <option value="yes">Yes</option>
244 </param>
245 </when>
246 </conditional>
247 <!-- Scaling data -->
248 <conditional name="scale_data_cond">
249 <param name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using the Normalization of ChIP-seq (NCIS) method.[2]">
250 <option value="no" selected="True">No</option>
251 <option value="yes">Yes</option>
252 </param>
253 <when value="yes">
254 <param name="scaling" type="select" label="Use signal vs control scaling?">
255 <option value="yes" selected="True">Yes</option>
256 <option value="no">No</option>
257 </param>
258 <param name="medianscale" type="select" label="Use the median signal/control ratio as the scaling factor?">
259 <option value="no" selected="True">No</option>
260 <option value="yes">Yes</option>
261 </param>
262 <param name="regressionscale" type="select" label="Use scaling by regression on binned tag counts?">
263 <option value="no" selected="True">No</option>
264 <option value="yes">Yes</option>
265 </param>
266 <param name="sesscale" type="select" label="Estimate scaling factor by SES?" help="SES: Diaz, et al. Stat Appl Genet Mol Biol. 2012">
267 <option value="no" selected="True">No</option>
268 <option value="yes">Yes</option>
269 </param>
270 <param name="fixedscaling" type="float" value="0.0" min="0.0" label="Multiply control counts by total tag count ratio and then by this factor" help="Set as 0 to skip" />
271 <param name="scalewin" type="integer" min="0" value="500" label="Window size for estimating scaling ratios" help="The value is the number of base pairs. Use something much smaller than the default if scaling via SES (e.g. 200)." />
272 <param name="plotscaling" type="select" label="Plot diagnostic information for the chosen scaling method?">
273 <option value="no" selected="True">No</option>
274 <option value="yes">Yes</option>
275 </param>
276 </when>
277 <when value="no" />
278 </conditional>
279 <!-- Running MultiGPS -->
280 <param name="readdistributionfile" type="data" optional="True" format="tabular" label="Optional binding event read distribution file for initializing models" help="A default initial distribution appropriate for ChIP-seq data is used if this option is not specified." />
281 <param name="maxtrainingrounds" type="integer" value="3" min="0" label="Maximum number of training rounds for updating binding event read distributions" />
282 <param name="nomodelupdate" type="select" label="Perform binding model updates?">
283 <option value="yes" selected="True">Yes</option>
284 <option value="no">No</option>
285 </param>
286 <param name="minmodelupdateevents" type="integer" value="500" min="0" label="Minimum number of events to support an update of the read distribution" />
287 <conditional name="binding_model_smoothing_cond">
288 <param name="nomodelsmoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline.">
289 <option value="yes" selected="True">Yes</option>
290 <option value="no">No</option>
291 </param>
292 <when value="yes">
293 <param name="splinesmoothparam" type="integer" value="30" min="0" label="Spline smoothing parameter" />
294 </when>
295 <when value="no" />
296 </conditional>
297 <conditional name="gauss_model_smoothing_cond">
298 <param name="gaussmodelsmoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline.">
299 <option value="no" selected="True">No</option>
300 <option value="yes">Yes</option>
301 </param>
302 <when value="no" />
303 <when value="yes">
304 <param name="gausssmoothparam" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." />
305 </when>
306 </conditional>
307 <param name="jointinmodel" type="select" label="Allow joint events in model updates?">
308 <option value="no" selected="True">No</option>
309 <option value="yes">Yes</option>
310 </param>
311 <param name="fixedmodelrange" type="select" label="Keep binding model range fixed to inital size?" help="Select No to vary automatically">
312 <option value="no" selected="True">No</option>
313 <option value="yes">Yes</option>
314 </param>
315 <param name="prlogconf" type="integer" value="-6" label="Poisson log threshold for potential region scanning" />
316 <param name="fixedalpha" type="integer" value="0" min="0" label="Impose this alpha" help="This is a sparse prior on binding events in the MultiGPS model. It can be interpreted as a minimum number of reads that each binding event must be responsible for in the model. A zero value will estimate the alpha automatically." />
317 <param name="alphascale" type="float" value="1.0" min="0" label="Alpha scaling factor" />
318 <param name="mlconfignotshared" type="select" label="Share component configs in the ML step?" help="Mainly affects the quantification of binding levels for binding events that are not shared but are located at nearby locations across experiments.">
319 <option value="yes" selected="True">Yes</option>
320 <option value="no">No</option>
321 </param>
322 <param name="exclude" type="data" optional="True" format="txt" label="Optional file containing a set of regions to ignore during MultiGPS training" help="Ideally exclude the mitochondrial genome and other blacklisted regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments." />
323 <!-- MultiGPS priors -->
324 <conditional name="use_motif_cond">
325 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
326 <option value="no" selected="True">No</option>
327 <option value="yes">Yes</option>
328 </param>
329 <when value="yes">
330 <!-- Specifying the genome -->
331 <conditional name="reference_genome_cond">
332 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
333 <option value="cached">locally cached</option>
334 <option value="history">from history</option>
335 </param>
336 <when value="cached">
337 <param name="reference_genome" type="select" label="Using reference genome">
338 <options from_data_table="all_fasta">
339 <!-- <filter type="data_meta" key="dbkey" ref="expt" column="1"/> does not yet work in a repeat...-->
340 </options>
341 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
342 </param>
343 </when>
344 <when value="history">
345 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
346 <options>
347 <!-- <filter type="data_meta" key="dbkey" ref="expt"/> does not yet work in a repeat...-->
348 </options>
349 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
350 </param>
351 </when>
352 </conditional>
353 <!-- MultiGPS priors options -->
354 <conditional name="multigps_priors_cond">
355 <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?">
356 <option value="no" selected="True">No</option>
357 <option value="yes">Yes</option>
358 </param>
359 <when value="no" />
360 <when value="yes">
361 <param name="noposprior" type="select" label="Perform inter-experiment positional prior?">
362 <option value="yes" selected="True">Yes</option>
363 <option value="no">No</option>
364 </param>
365 <param name="probshared" type="float" value="0.9" min="0.0" label="Probability that events are shared across conditions" />
366 <conditional name="both_motifs_cond">
367 <param name="nomotifs" type="select" label="Perform both motif-finding and motif priors?">
368 <option value="yes" selected="True">Yes</option>
369 <option value="no">No</option>
370 </param>
371 <when value="yes">
372 <expand macro="motif_finding_params" />
373 </when>
374 <when value="no">
375 <conditional name="nomotifprior_cond">
376 <param name="nomotifprior" type="select" label="Perform motif-finding only?" help="Selecting Yes turns off motif priors.">
377 <option value="no" selected="True">No</option>
378 <option value="yes">Yes</option>
379 </param>
380 <when value="no" />
381 <when value="yes">
382 <expand macro="motif_finding_params" />
383 </when>
384 </conditional>
385 </when>
386 </conditional>
387 </when>
388 </conditional>
389 </when>
390 <when value="no" />
391 </conditional>
392 <!-- Reporting binding events -->
393 <conditional name="report_binding_events_cond">
394 <param name="report_binding_events" type="select" label="Report binding events?">
395 <option value="no" selected="True">No</option>
396 <option value="yes">Yes</option>
397 </param>
398 <when value="no" />
399 <when value="yes">
400 <param name="minqvalue" type="float" min="0" value="0.001" label="Minimum Q-value (corrected p-value) of reported binding events" />
401 <param name="minfold" type="float" min="0" value="1.5" label="Minimum event fold-change vs scaled control" />
402 <param name="nodifftests" type="select" label="Run differential enrichment tests?">
403 <option value="yes" selected="True">Yes</option>
404 <option value="no">No</option>
405 </param>
406 <param name="edgerod" type="float" min="0" value="0.15" label="EdgeR over-dispersion parameter value" />
407 <param name="diffp" type="float" min="0" value="0.01" label="Minimum p-value for reporting differential enrichment" />
408 </when>
409 </conditional>
410 </when>
411 <when value="hide" />
412 </conditional>
413 </inputs>
414 <outputs>
415 <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">
416 <filter>save_design_file == 'yes'</filter>
417 </data>
418 <data name="output_bed" format="bed" label="${tool.name} (bed) on ${on_string}"/>
419 <data name="output_html" format="html" label="${tool.name} (html) on ${on_string}"/>
420 <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/>
421 <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/>
422 </outputs>
423 <tests>
424 <test>
425 <repeat name="condition_repeat">
426 <repeat name="signal_repeat">
427 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
428 </repeat>
429 </repeat>
430 <param name="advanced_options" value="hide" />
431 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
432 <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>
433 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
434 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
435 </test>
436 <test>
437 <repeat name="condition_repeat">
438 <repeat name="signal_repeat">
439 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
440 </repeat>
441 <repeat name="control_repeat">
442 <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
443 </repeat>
444 </repeat>
445 <param name="advanced_options" value="display" />
446 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
447 <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>
448 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
449 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
450 </test>
451 </tests>
452 <help>
453
454 **What it does**
455
456 MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing
457 differential binding events between conditions. MultiGPS encourages consistency in the reported binding
458 event locations across conditions and provides accurate estimation of ChIP enrichment levels at each event.
459 MultiGPS performs significant EM optimization of binding events along the genome and across experimental
460 conditions, and it integrates motif-finding via MEME. The tool loads all data into memory, so the potential
461 exists for time and memory intensive analyses if running over many conditions or large datasets.
462
463 -----
464
465 **Options**
466
467 * **Loading data:**
468
469 - **Optional file containing reads from a control experiment** - file containing reads from a control experiment
470 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
471 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
472 - **Use non-unique reads** - Use non-unique reads.
473 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments
474 - **Turn off caching of the entire set of experiments?** - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory).
475
476 * **Scaling control vs signal counts:**
477
478 - **Use signal vs control scaling?** - Flag to turn off auto estimation of signal vs control scaling factor
479 - **Use the median signal/control ratio as the scaling factor?** - Flag to use scaling by median ratio (default = scaling by NCIS).
480 - **Use scaling by regression on binned tag counts?** - Flag to use scaling by regression (default = scaling by NCIS).
481 - **Estimate scaling factor by SES?** - Specify whether to estimate scaling factor by SES.
482 - **Multiply control counts by total tag count ratio and then by this factor** - Multiply control counts by total tag count ratio and then by this factor (default: NCIS).
483 - **Window size for estimating scaling ratios** - Window size in base pairs for estimating scaling ratios
484 - **Plot diagnostic information for the chosen scaling method?** - Flag to plot diagnostic information for the chosen scaling method.
485
486 * **Running MultiGPS:**
487
488 - **Optional binding event read distribution file** - Binding event read distribution file for initializing models. The true distribution of reads around binding events is estimated during MultiGPS training. A default initial distribution appropriate for ChIP-seq data is used if this option is not specified.
489 - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions.
490 - **Perform binding model updates?** - Perform binding model updates?
491 - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution
492 - **Perform binding model smoothing?** - Smooth with a cubic spline using a specified smoothing factor.
493 - **Spline smoothing parameter** - Smoothing parameter for smoothing cubic spline.
494 - **Perform Gaussian model smoothing?** - Select "Yes" to use Gaussian model smoothing using a specified smoothing factor if binding model smoothing is not performed.
495 - **Allow joint events in model updates?** - Specify whether to allow joint events in model updates.
496 - **Keep binding model range fixed to inital size?** - Flag to keep binding model range fixed to inital size (default: vary automatically)
497 - **Poisson log threshold for potential region scanning** - Poisson log threshold for potential region scanning.
498 - **Alpha scaling factor** - Alpha scaling factor. Increasing this parameter results in stricter binding event calls.
499 - **Impose this alpha** - The alpha parameter is a sparse prior on binding events in the MultiGPS model. It can be interpreted as a minimum number of reads that each binding event must be responsible for in the model. Default: estimate alpha automatically.
500 - **Share component configs in the ML step?** - Flag to not share component configs in the ML step
501 - **Optional file containing a set of regions to ignore during MultiGPS training** - File containing a set of regions to ignore during MultiGPS training. It’s a good idea to exclude the mitochondrial genome and other ‘blacklisted’ regions that contain artifactual accumulations of reads in both ChIP-seq and control experiments. MultiGPS will waste time trying to model binding events in these regions, even though they will not typically appear significantly enriched over the control (and thus will not be reported to the user).
502
503 * **MultiGPS priors:**
504
505 - **Perform inter-experiment positional prior?** - Flag to turn off inter-experiment positional prior (default=on).
506 - **Probability that events are shared across conditions** - Probability that events are shared across conditions.
507 - **Perform both motif-finding and motif priors?** - Flag to turn off motif-finding and motif priors.
508 - **Perform motif-finding only?** - Flag to turn off motif priors only.
509 - **Number of motifs MEME should find for each condition** - Number of motifs MEME should find for each condition.
510 - **Minimum motif width for MEME** - minw arg for MEME.
511 - **Maximum motif width for MEME** - maxw arg for MEME.
512
513 * **Reporting binding events:**
514
515 - **Minimum Q-value (corrected p-value) of reported binding events** - Minimum Q-value (corrected p-value) of reported binding events.
516 - **Minimum event fold-change vs scaled control** - Minimum event fold-change vs scaled control.
517 - **Run differential enrichment tests?** - Choose whether to run differential enrichment tests.
518 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value.
519 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.
520
521 </help>
522 <citations>
523 <citation type="bibtex">
524 @article{Mahony2014,
525 journal = {PLOS Computational Biology},
526 author = {1. Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK},
527 title = {An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding},
528 year = {2014},}
529 volume = {10},
530 number = {3},
531 pages = {e1003501},}
532 </citation>
533 <citation type="bibtex">
534 @article{Liang2012,
535 journal = {BMC Bioinformatics},
536 author = {2. Liang, Ketes},
537 title = {Normalization of ChIP-seq data with control},
538 year = {2012},}
539 </citation>
540 </citations>
541 </tool>
542