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author greg
date Sat, 02 Jan 2016 14:07:37 -0500
parents f52d31a2c386
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4:32cff4d1d0ff 5:7b15099378a7
1 <tool id="multigps" name="MultiGPS" version="0.5.0.0"> 1 <tool id="multigps" name="MultiGPS" version="0.5.0.0">
2 <description>analyzes collections of multi-condition ChIP-seq data</description> 2 <description>analyzes collections of multi-condition ChIP-seq data</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="4.11.0">meme</requirement> 4 <import>multigps_macros.xml</import>
5 <requirement type="package" version="3.11.0">edger</requirement> 5 </macros>
6 <requirement type="package" version="2.14">biocbasics</requirement> 6 <expand macro="requirements" />
7 </requirements>
8 <command> 7 <command>
9 <![CDATA[ 8 <![CDATA[
10 mkdir multigps_out && 9 #set aoc = $advanced_options_cond
11 java -jar $__tool_directory__/multigps_v0.5.jar 10 #if str($aoc.advanced_options) == "display":
11 #set umc = $aoc.use_motif_cond
12 #set rgc = $umc.reference_genome_cond
13 #if str($umc.use_motif) == "yes":
14 #if str($rgc.reference_genome_source) == "cached":
15 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
16 #else:
17 ## MultiGPS requires a directory containing reference files, so symlink the history dataset.
18 #import os
19 #import tempfile
20 #set seq_dir = tempfile.mkdtemp(prefix="tmp-multigps-seq-dir")
21 #set seq_file = str($rgc.reference_genome)
22 #set tmp_filename = "%s.fa" % str($rgc.reference_genome.dbkey)
23 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename)
24 ln -f -s $tmp_seq_file $seq_file &&
25 #end if
26 #end if
27 #end if
28 python $__tool_directory__/multigps.py
29 --multigps_jar $__tool_directory__/multigps_v0.5.jar
30 #for $i in $input_items:
31 #set replicate_name = ""
32 #set read_distribution_file = ""
33 #set fixed_read = ""
34 #set sccond = $i.signal_control_cond
35 #set sorc = $sccond.signal_control
36 #if str($sorc) == "Signal":
37 #set replicate_name = $sccond.replicate_name
38 #set rdcond = $sccond.read_distribution_cond
39 #if str($rdcond.read_distribution) == "yes":
40 #set read_distribution_file = "$rdcond.read_distribution_file"
41 #end if
42 #if str($sccond.fixed_read_count) == "yes":
43 #set fixed_read = "P"
44 #end if
45 #else if str($sorc) == "Control":
46 #set rncond = $sccond.replicate_name_cond
47 #if str($rncond.specify_replicate_name) == "yes":
48 #set replicate_name = $rncond.replicate_name
49 #set rdcond = $rncond.read_distribution_cond
50 #if str($rdcond.read_distribution) == "yes":
51 #set read_distribution_file = "$rdcond.read_distribution_file"
52 #end if
53 #if str($rncond.fixed_read_count) == "yes":
54 #set fixed_read = "P"
55 #end if
56 #end if
57 #end if
58 --input_item "${i.input}" "${i.input.ext}" "${i.signal_control_cond.signal_control}" "${i.condition_name}" "$replicate_name" "$read_distribution_file" "$fixed_read"
59 #end for
12 --threads="\${GALAXY_SLOTS:-4}" 60 --threads="\${GALAXY_SLOTS:-4}"
13 --verbose 61 --geninfo $chromInfo
14 --geninfo ${chromInfo} 62 #if str($aoc.advanced_options) == "display":
15 #if str($use_motif_cond.use_motif) == "yes": 63 #set rbec = $aoc.report_binding_events_cond
16 #set seq_dir = python "$get_seq_dir" 64 #set bmsc = $aoc.binding_model_smoothing_cond
17 --seq "${seq_dir}" 65 #set rloc = $aoc.reads_limits_options_cond
18 --mememinw $use_motif_cond.min_motif_width 66 #set sdc = $aoc.scale_data_cond
19 --mememaxw $use_motif_cond.max_motif_width 67 --use_motif $umc.use_motif
20 --design $design_file 68 #if str($umc.use_motif) == "yes":
21 #if str($gauss_model_smoothing_cond.gauss_model_smoothing) == "yes": 69 #set mpc = $umc.multigps_priors_cond
22 --gaussmodelsmoothing 70 --seq_dir $seq_dir
23 --gausssmoothparam $gauss_model_smoothing_cond.gauss_model_smoothing.gauss_smooth 71 #if str($mpc.multigps_priors) == "yes":
72 #set bmc = $mpc.both_motifs_cond
73 --positional_prior $mpc.positional_prior
74 --events_shared_probability $mpc.events_shared_probability
75 --motifs $bmc.motifs
76 #if str($bmc.motifs) == "yes":
77 --num_motifs $bmc.num_motifs
78 --mememinw $bmc.min_motif_width
79 --mememaxw $bmc.max_motif_width
80 #else:
81 #set mfoc = $bmc.motif_finding_only_cond
82 --motif_finding_only $mfoc.motif_finding_only
83 #if str($mfoc.motif_finding_only) == "yes":
84 --num_motifs $mfoc.num_motifs
85 --mememinw $mfoc.min_motif_width
86 --mememaxw $mfoc.max_motif_width
87 #end if
88 #end if
89 #end if
90 #end if
91 --max_training_rounds $aoc.max_training_rounds
92 --exclude_file $aoc.exclude_file
93 --binding_model_updates $aoc.binding_model_updates
94 --minmodelupdateevents $aoc.minmodelupdateevents
95 --binding_model_smoothing $bmsc.binding_model_smoothing
96 #if str($bmsc.binding_model_smoothing) == "yes":
97 --spline_smooth $bmsc.spline_smooth
98 #else:
99 #set gmsc = $bmsc.gauss_model_smoothing_cond
100 #if str($gmsc.gauss_model_smoothing) == "yes":
101 --gauss_smooth $gmsc.gauss_smooth
102 #end if
103 #end if
104 --joint_in_model $aoc.joint_in_model
105 --ml_config_not_shared $aoc.ml_config_not_shared
106 #if str($rloc.reads_limits) == "yes":
107 --fixedpb $rloc.fixedpb
108 --poissongausspb $rloc.poissongausspb
109 --non_unique_reads $rloc.non_unique_reads
110 #end if
111 #if str($rbec.report_binding_events) == "yes":
112 --minqvalue $rbec.minqvalue
113 --minfold $rbec.minfold
114 --diff_enrichment_tests $rbec.diff_enrichment_tests
115 --edgerod $rbec.edgerod
116 --diffp $rbec.diffp
117 #end if
118 #if str($sdc.scale_data) == "yes":
119 --noscaling $sdc.scaling
120 --medianscale $sdc.medianscale
121 --sesscale $sdc.sesscale
122 --scalewin $sdc.scalewin
123 #end if
24 #end if 124 #end if
25 --out multigps_out 125 --output_html_path "$output_html"
126 --output_html_files_path "$output_html.files_path"
127 #if str($output_process_log) == "yes":
128 --output_process_path "$output_process"
129 #end if
26 ]]> 130 ]]>
27 </command> 131 </command>
28 <configfiles>
29 <configfile name="design_file">
30 <![CDATA[
31 #for input in $input_files:
32 #set filename = "{$input['input'].filename}"
33 #set signal_control = $input['signal_control']
34 #set format = $input['input'].ext
35 #set condition_name = $input['condition_name']
36 #set replicate_name = $input['replicate_name']
37 #set line = '\t'.join($filename, $signal_control, $format, $condition_name, $replicate_name])
38 ${line}
39 #end for
40 ]]>
41 </configfile>
42 <configfile name="get_seq_dir">
43 <![CDATA[
44 #!/usr/bin/env python
45 import os
46 import tempfile
47
48 # All inputs must have the same dbkey, and MultiGPS requires a directory, not the reference file.
49 if $use_motif_cond.reference_genome_cond.reference_genome_source == "cached":
50 return os.path.split($use_motif_cond.reference_genome_cond.reference_genome.fields.path)[0]
51 else:
52 seq_dir = tempfile.mkdtemp(prefix="tmp-multigps-")
53 # Populate the directory with the history dataset
54 tmp_filename = "%s.fa" % $use_motif_cond.reference_genome_cond.reference_genome.dbkey
55 ln -f -s $use_motif_cond.reference_genome_cond.reference_genome.filename os.path.join(seq_dir, tmp_filename)
56 return seq_dir
57 ]]>
58 </configfile>
59 </configfiles>
60 <inputs> 132 <inputs>
61 <repeat name="input_files" title="Input Files" min="1"> 133 <repeat name="input_items" title="Input files, attributes and options" min="1">
62 <param name="input" type="data" format="bam,bed,scidx" label="Add file"> 134 <param name="input" type="data" format="bam,bed,scidx" label="Add input file" help="Supported formats are bam, bed and scidx">
63 <validator type="unspecified_build" /> 135 <validator type="unspecified_build" />
64 </param> 136 </param>
65 <param name="signal_control" type="select" label="Signal or control" display="checkboxes" > 137 <conditional name="signal_control_cond">
66 <option value="signal" selected="True">Signal</option> 138 <param name="signal_control" type="select" label="Is this experiment signal or control?">
67 <option value="control">Control</option> 139 <option value="Signal" selected="True">Signal</option>
140 <option value="Control">Control</option>
141 </param>
142 <when value="Signal">
143 <param name="replicate_name" type="text" label="Replicate name" />
144 <expand macro="rd_cond" />
145 <expand macro="frc_param" />
146 </when>
147 <when value="Control">
148 <conditional name="replicate_name_cond">
149 <param name="specify_replicate_name" type="select" label="Specify replicate name?" help="Optional for control experiments. If used, the control will only be used for the corresponding named signal replicate">
150 <option value="no" selected="True">No</option>
151 <option value="yes">Yes</option>
152 </param>
153 <when value="yes">
154 <param name="replicate_name" type="text" optional="True" label="Replicate name" />
155 <expand macro="rd_cond" />
156 <expand macro="frc_param" />
157 </when>
158 <when value="no" />
159 </conditional>
160 </when>
161 </conditional>
162 <param name="condition_name" type="text" label="Condition name" />
163 </repeat>
164 <conditional name="advanced_options_cond">
165 <param name="advanced_options" type="select" label="Advanced options">
166 <option value="hide" selected="true">Hide</option>
167 <option value="display">Display</option>
68 </param> 168 </param>
69 <param label="Condition name" name="condition_name" type="text" /> 169 <when value="display">
70 <param label="Replicate name" name="replicate_name" type="text" /> 170 <conditional name="use_motif_cond">
71 171 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
72 <conditional name="use_motif_cond"> 172 <option value="no" selected="True">No</option>
73 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?"> 173 <option value="yes">Yes</option>
174 </param>
175 <when value="yes">
176 <conditional name="reference_genome_cond">
177 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
178 <option value="cached">Locally Cached</option>
179 <option value="history">From History</option>
180 </param>
181 <when value="cached">
182 <param name="reference_genome" type="select" label="Using reference genome">
183 <options from_data_table="fasta_indexes"/>
184 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
185 </param>
186 </when>
187 <when value="history">
188 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"/>
189 </when>
190 </conditional>
191 <conditional name="multigps_priors_cond">
192 <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?">
193 <option value="no" selected="True">No</option>
194 <option value="yes">Yes</option>
195 </param>
196 <when value="no" />
197 <when value="yes">
198 <param name="positional_prior" type="select" label="Perform inter-experiment positional prior?">
199 <option value="yes" selected="True">Yes</option>
200 <option value="no">No</option>
201 </param>
202 <param name="events_shared_probability" type="float" value="0.9" min="0.0" label="Probability that events are shared across conditions" />
203 <conditional name="both_motifs_cond">
204 <param name="motifs" type="select" label="Perform both motif-finding and motif priors?">
205 <option value="yes" selected="True">Yes</option>
206 <option value="no">No</option>
207 </param>
208 <when value="yes">
209 <expand macro="motif_finding_params" />
210 </when>
211 <when value="no">
212 <conditional name="motif_finding_only_cond">
213 <param name="motif_finding_only" type="select" label="Perform motif-finding only?" help="Selecting Yes turns off motif priors.">
214 <option value="no" selected="True">No</option>
215 <option value="yes">Yes</option>
216 </param>
217 <when value="no" />
218 <when value="yes">
219 <expand macro="motif_finding_params" />
220 </when>
221 </conditional>
222 </when>
223 </conditional>
224 </when>
225 </conditional>
226 </when>
227 <when value="no" />
228 </conditional>
229 <param name="max_training_rounds" type="integer" value="3" min="0" label="Maximum number of training rounds for updating binding event read distributions" />
230 <param name="exclude_file" 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." />
231 <param name="binding_model_updates" type="select" label="Perform binding model updates?">
74 <option value="yes" selected="True">Yes</option> 232 <option value="yes" selected="True">Yes</option>
75 <option value="no">No</option> 233 <option value="no">No</option>
76 </param> 234 </param>
77 <when value="yes"> 235 <param name="minmodelupdateevents" type="integer" value="0" min="0" label="Minimum number of events to support an update of the read distribution" />
78 <conditional name="reference_genome_cond"> 236 <conditional name="binding_model_smoothing_cond">
79 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome"> 237 <param name="binding_model_smoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline.">
80 <option value="cached">Locally Cached</option> 238 <option value="yes" selected="True">Yes</option>
81 <option value="history">From History</option> 239 <option value="no">No</option>
82 </param> 240 </param>
83 <when value="cached"> 241 <when value="yes">
84 <param name="reference_genome" type="select" label="Using reference genome"> 242 <param name="spline_smooth" type="integer" value="0" min="0" label="Smoothing factor" />
85 <options from_data_table="fasta_indexes"/> 243 </when>
86 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 244 <when value="no">
245 <conditional name="gauss_model_smoothing_cond">
246 <param name="gauss_model_smoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline.">
247 <option value="no" selected="True">No</option>
248 <option value="yes">Yes</option>
87 </param> 249 </param>
88 </when> 250 <when value="yes">
89 <when value="history"> 251 <param name="gauss_smooth" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." />
90 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"/> 252 </when>
91 </when> 253 <when value="no" />
92 </conditional> 254 </conditional>
93 <param name="min_motif_width" type="integer" min="0" value="6" label="Minimum motif width for MEME"/> 255 </when>
94 <param name="max_motif_width" type="integer" min="0" value="16" label="Maximum motif width for MEME"/> 256 </conditional>
95 </when> 257 <param name="joint_in_model" type="select" label="Allow joint events in model updates?">
96 <when value="no"/> 258 <option value="no" selected="True">No</option>
97 </conditional> 259 <option value="yes">Yes</option>
98 </repeat> 260 </param>
99 <param name="genome_info_file" type="data" format="tabular" label="Genome information dataset" help="What's this? See the help section below."/> 261 <param name="ml_config_not_shared" type="select" label="Share component configs in the ML step?">
100 <conditional name="gauss_model_smoothing_cond"> 262 <option value="yes" selected="True">Yes</option>
101 <param name="gauss_model_smoothing" type="select" label="Turn on Gaussian model smoothing?" help="Smoothing is done with a cubic spline."> 263 <option value="no">No</option>
102 <option value="yes" selected="True">Yes</option> 264 </param>
103 <option value="no">No</option> 265 <conditional name="reads_limits_options_cond">
104 </param> 266 <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.">
105 <when value="yes"> 267 <option value="no" selected="True">No</option>
106 <param name="gauss_smooth" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." /> 268 <option value="yes">Yes</option>
269 </param>
270 <when value="no" />
271 <when value="yes">
272 <param name="fixedpb" type="integer" value="0" min="0" label="Fixed per-base limit" />
273 <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" />
274 <param name="non_unique_reads" type="select" label="Use non-unique reads">
275 <option value="no" selected="True">No</option>
276 <option value="yes">Yes</option>
277 </param>
278 </when>
279 </conditional>
280 <conditional name="scale_data_cond">
281 <param name="scale_data" type="select" label="Set data scaling parameters?" help="Default behavior is to scale signal to corresponding controls using regression on the set of signal/control ratios in 10Kbp windows.">
282 <option value="no" selected="True">No</option>
283 <option value="yes">Yes</option>
284 </param>
285 <when value="yes">
286 <param name="scaling" type="select" label="Use signal vs control scaling?">
287 <option value="yes" selected="True">Yes</option>
288 <option value="no">No</option>
289 </param>
290 <param name="medianscale" type="select" label="Use the median signal/control ratio as the scaling factor?">
291 <option value="yes" selected="True">Yes</option>
292 <option value="no">No</option>
293 </param>
294 <param name="sesscale" type="select" label="Estimate scaling factor by SES?" help="SES: Diaz, et al. Stat Appl Genet Mol Biol. 2012">
295 <option value="yes" selected="True">Yes</option>
296 <option value="no">No</option>
297 </param>
298 <param name="scalewin" type="integer" min="0" value="10000" 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)." />
299 </when>
300 <when value="no" />
301 </conditional>
302 <conditional name="report_binding_events_cond">
303 <param name="report_binding_events" type="select" label="Report binding events?">
304 <option value="no" selected="True">No</option>
305 <option value="yes">Yes</option>
306 </param>
307 <when value="no" />
308 <when value="yes">
309 <param name="minqvalue" type="integer" min="0" value="0" label="Minimum Q-value (corrected p-value) of reported binding events" />
310 <param name="minfold" type="integer" min="0" value="0" label="Minimum event fold-change vs scaled control" />
311 <param name="diff_enrichment_tests" type="select" label="Run differential enrichment tests?">
312 <option value="yes" selected="True">Yes</option>
313 <option value="no">No</option>
314 </param>
315 <param name="edgerod" type="integer" min="0" value="0" label="EdgeR over-dispersion parameter value" />
316 <param name="diffp" type="integer" min="0" value="0" label="Minimum p-value for reporting differential enrichment" />
317 </when>
318 </conditional>
107 </when> 319 </when>
108 <when value="no" /> 320 <when value="hide"/>
109 </conditional> 321 </conditional>
322 <param name="output_process_log" type="select" label="Output MultiGPS process log?">
323 <option value="no" selected="True">No</option>
324 <option value="yes">Yes</option>
325 </param>
110 </inputs> 326 </inputs>
111 <outputs> 327 <outputs>
112 <data name="output_report" format="txt" label="MultiGPS-Report"/> 328 <data name="output_process" format="txt" label="${tool.name} on ${on_string} (process log)">
113 <data name="output_gff" format="gff" label="MultiGPS-GFF" /> 329 <filter>output_process_log == "yes"</filter>
114 <data name="output_gz" format="gz" label="MultiGPS-GZ" /> 330 </data>
331 <data name="output_html" format="html"/>
115 </outputs> 332 </outputs>
333 <tests>
334 <test>
335 <repeat name="input_items">
336 <param name="input" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/>
337 <param name="signal_control" value="Signal"/>
338 <param name="condition_name" value="Abf1"/>
339 <param name="replicate_name" value="1"/>
340 <param name="read_distribution" value="no"/>
341 <param name="fixed_read_count" value="no"/>
342 </repeat>
343 <param name="binding_model_smoothing" value="no"/>
344 <param name="gauss_model_smoothing" value="yes"/>
345 <param name="gauss_smooth" value="3"/>
346 <param name="use_motif" value="yes"/>
347 <param name="reference_genome_source" value="history"/>
348 <param name="reference_genome" value="phiX.fasta" dbkey="phiX"/>
349 <param name="num_motifs" value="3"/>
350 <param name="min_motif_width" value="6"/>
351 <param name="max_motif_width" value="16"/>
352 <param name="output_process_log" value="yes"/>
353 <output name="output_process" file="output_process1.txt" ftype="txt" lines_diff="12"/>
354 <output name="output_html" file="output_html1.html" ftype="html" lines_diff="12"/>
355 </test>
356 </tests>
116 <help> 357 <help>
117 358
118 **What it does** 359 **What it does**
119 360
120 MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing 361 MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing
125 366
126 ----- 367 -----
127 368
128 **Options** 369 **Options**
129 370
130 * **Input Files** 371 * **Input files, attributes and options**
372
373 - **Is this experiment signal or control?** - Designate the associated input file as a “signal” or “control” experiment.
374 - **Condition name** - Condition name.
375 - **Replicate name** - This is optional for control experiments, and if defined, the control will only be used for the corresponding named signal replicate.
376 - **Read distribution file** - Optional binding event read distribution file (appropriate for the specified replicate) for initializing models. If not specified, the default distribution is used. The true distribution of reads around binding events is estimated during MultiGPS training.
377 - **Use fixed per-base read count limit for this replicate?** - Optional fixed per-base read count limit for the specified replicate. Selecting "Yes" sets a read count limit that varies along the genome according to how neighboring bases are distributed, while selecting "No" sets a global per-base limit that is estimated from a Poisson distribution.
378
379 * **Perform motif-finding or use a motif-prior?** - Integrate motif-finding or use a motif-prior via MEME.
380
381 - **Choose the source for the reference genome** - Reference data can be locally cached or selected from the Galaxy history.
382 - **Perform inter-experiment positional prior?** - Perform inter-experiment positional prior.
383 - **Probability that events are shared across conditions** - Probability that events are shared across conditions.
384 - **Perform both motif-finding and motif priors?** - Select "No" to turn off motif-finding and motif priors.
385 - **Perform motif-finding only?** - Select "Yes" to turn off motif priors, performing motif-finding only.
386 - **Number of motifs MEME should find for each condition** - Number of motifs MEME should find for each condition.
387 - **Minimum motif width for MEME** - Minimum motif width argument for MEME.
388 - **Maximum motif width for MEME** - Maximum motif width argument for MEME.
389
390 * **General Advanced Options**
391
392 - **Maximum number of training rounds for updating binding event read distributions** - Maximum number of training rounds for updating binding event read distributions
393 - **Optional 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).
394 - **Perform binding model updates?** - Perform binding model updates?
395 - **Minimum number of events to support an update of the read distribution** - Minimum number of events to support an update of the read distribution
396 - **Perform binding model smoothing?** - Smooth with a cubic spline using a specified smoothing factor.
397 - **Perform Gaussian model smoothing?** - Select "Yes" to use Gaussian model smoothing using a specified smoothing factor if binding model smoothing is not performed.
398 - **Allow joint events in model updates?** - Specify whether to allow joint events in model updates.
399 - **Share component configs in the ML step?** - Specify whether to share component configs in the ML step. This mainly affects the quantification of binding levels for binding events that are not shared but are located at nearby locations across experiments.
400
401 * **Set limits on how many reads can have their 5′ end at the same position in each replicate?**
402
403 - **Fixed per-base limit** - Fixed per-base limit.
404 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
405 - **Use non-unique reads** - Use non-unique reads.
406
407 * **Set data scaling parameters?**
408
409 - **Use signal vs control scaling?** - Specify whether to use signal vs control scaling.
410 - **Use the median signal/control ratio as the scaling factor?** - Specify whether to use the median signal/control ratio as the scaling factor.
411 - **Estimate scaling factor by SES?** - Specify whether to estimate scaling factor by SES.
412 - **Window size for estimating scaling ratios** - Window size in base pairs for estimating scaling ratios
413
414 * **Report binding events?**
415
416 - **Minimum Q-value (corrected p-value) of reported binding events** - Minimum Q-value (corrected p-value) of reported binding events.
417 - **Minimum event fold-change vs scaled control** - Minimum event fold-change vs scaled control.
418 - **Run differential enrichment tests?** - Choose whether to run differential enrichment tests.
419 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value.
420 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.
421
422 * **Output MultiGPS process log?** - Select "Yes" to produce a second output dataset that contains the MultiGPS process log.
131 423
132 </help> 424 </help>
133 <citations> 425 <expand macro="citations" />
134 <citation type="doi">10.1371/journal.pcbi.1003501</citation>
135 </citations>
136 </tool> 426 </tool>