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author greg
date Tue, 13 Dec 2016 13:02:36 -0500
parents 426f8753acb2
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17:426f8753acb2 18:e3d9e74cae68
1 <tool id="multigps" name="MultiGPS" version="0.5.0.0"> 1 <tool id="multigps" name="MultiGPS" version="0.72.0">
2 <description>analyzes collections of multi-condition ChIP-seq data</description> 2 <description>analyzes collections of multi-condition ChIP-seq data</description>
3 <macros> 3 <macros>
4 <import>multigps_macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="aggressive">
7 <command> 8 <command>
8 <![CDATA[ 9 <![CDATA[
10 ## java -Xmx15G org.seqcode.projects.multigps.MultiGPS
11 ## --species "Saccharomyces cerevisiae;sacCer3"
12 ## --threads 2
13 ## --expt $bampath/$name.bam
14 ## --ctrl $control
15 ## --format BAM
16 ## --scalewin 500
17 ## --q 0.05
18 ## --nodifftests
19 ## --verbose
20 ## --mappability
21 ## --jointinmodel
22 ## --fixedmodelrange
23 ## --gaussmodelsmoothing
24 ## --gausssmoothparam 1
25 ## --minmodelupdateevents 50
26 ## --memepath $memePath
27 ## --mememinw 6
28 ## --mememaxw 18
29 ## --seq $genome
30 ## --exclude $exclude
31 ## --out $name > $name.out 2>&1
32 ##
33
34 multigps
35 ############################
36 ## General options
37 ############################
38 --input "$input"
39 --format "$input.ext"
40 #if str($verbose) == 'yes':
41 --verbose
42 #end if
43 --threads="\${GALAXY_SLOTS:-4}"
44 ############################
45 ## Advanced options
46 ############################
9 #set aoc = $advanced_options_cond 47 #set aoc = $advanced_options_cond
10 #if str($aoc.advanced_options) == "display": 48 #if str($aoc.advanced_options) == "display":
49 #set bmsc = $aoc.binding_model_smoothing_cond
50 #set gmsc = $aoc.gauss_model_smoothing_cond
51 #set rbec = $aoc.report_binding_events_cond
52 #set rloc = $aoc.reads_limits_options_cond
53 #set sdc = $aoc.scale_data_cond
11 #set umc = $aoc.use_motif_cond 54 #set umc = $aoc.use_motif_cond
55 ############################
56 ## Limits on how many reads
57 ############################
58 #if str($rloc.reads_limits) == "yes":
59 --fixedpb $rloc.fixedpb
60 --poissongausspb $rloc.poissongausspb
61 #if str($rloc.nonunique) == "yes":
62 --nonunique
63 #end if
64 --mappability $rloc.mappability
65 #end if
66 #if str($rloc.nocache) == "yes":
67 --nocache
68 #end if
69 ############################
70 ## Scaling data
71 ############################
72 #if str($sdc.scale_data) == "yes":
73 #if str($sdc.scaling) == 'no':
74 --noscaling $sdc.scaling
75 #end if
76 #if str($sdc.medianscale) == 'yes':
77 --medianscale $sdc.medianscale
78 #end if
79 #if str($sdc.regressionscale) == 'yes':
80 --regressionscale $sdc.regressionscale
81 #endif
82 #if str($sdc.sessscale) == 'yes':
83 --sesscale $sdc.sesscale
84 #end if
85 #if $sdc.fixedscaling > 0:
86 ‒‒fixedscaling $sdc.fixedscaling
87 #end if
88 --scalewin $sdc.scalewin
89 #if str($sdc.plotscaling) == 'yes':
90 --plotscaling $sdc.plotscaling
91 #end if
92 #end if
93 ############################
94 ## Running MultiGPS
95 ############################
96 #if str($aoc.nomodelupdate) == "no":
97 --nomodelupdate
98 #end if
99 --minmodelupdateevents $aoc.minmodelupdateevents
100 #if str($bmsc.nomodelsmoothing) == "no":
101 --nomodelsmoothing
102 #end if
103 --splinesmoothparam $aoc.splinesmoothparam
104 #if str($gmsc.gaussmodelsmoothing) == "yes":
105 --gaussmodelsmoothing
106 --gausssmoothparam $gmsc.gausssmoothparam
107 #end if
108 #if str($aoc.jointinmodel) == "yes":
109 --jointinmodel
110 #end if
111 #if str($aoc.fixedmodelrange) == "yes":
112 --fixedmodelrange
113 #end if
114 --prlogconf $aoc.prlogconf
115 #if $aoc.fixedalpha > 0:
116 --fixedalpha $aoc.fixedalpha
117 #end if
118 --alphascale $aoc.alphascale
119 #if str($aoc.mlconfignotshared) == "no":
120 --mlconfignotshared
121 #end if
122 --exclude "$aoc.exclude"
123 ############################
124 ## MultiGPS priors
125 ############################
12 #if str($umc.use_motif) == "yes": 126 #if str($umc.use_motif) == "yes":
13 #set rgc = $umc.reference_genome_cond 127 #set rgc = $umc.reference_genome_cond
14 #if str($rgc.reference_genome_source) == "cached": 128 #if str($rgc.reference_genome_source) == "cached":
15 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] 129 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
16 #else: 130 #else:
21 #set seq_file = str($rgc.reference_genome) 135 #set seq_file = str($rgc.reference_genome)
22 #set tmp_filename = "%s.fa" % str($rgc.reference_genome.dbkey) 136 #set tmp_filename = "%s.fa" % str($rgc.reference_genome.dbkey)
23 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename) 137 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename)
24 ln -f -s $tmp_seq_file $seq_file && 138 ln -f -s $tmp_seq_file $seq_file &&
25 #end if 139 #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
60 --threads="\${GALAXY_SLOTS:-4}"
61 --geninfo $chromInfo
62 #if str($aoc.advanced_options) == "display":
63 #set rbec = $aoc.report_binding_events_cond
64 #set bmsc = $aoc.binding_model_smoothing_cond
65 #set rloc = $aoc.reads_limits_options_cond
66 #set sdc = $aoc.scale_data_cond
67 --use_motif $umc.use_motif
68 #if str($umc.use_motif) == "yes":
69 #set mpc = $umc.multigps_priors_cond 140 #set mpc = $umc.multigps_priors_cond
70 --seq_dir $seq_dir 141 --seq $seq_dir
142 --geninfo ${chromInfo}
71 #if str($mpc.multigps_priors) == "yes": 143 #if str($mpc.multigps_priors) == "yes":
72 #set bmc = $mpc.both_motifs_cond 144 #set bmc = $mpc.both_motifs_cond
73 --positional_prior $mpc.positional_prior 145 #if str($mpc.noposprior) == "no":
74 --events_shared_probability $mpc.events_shared_probability 146 --noposprior
75 --motifs $bmc.motifs 147 #end if
76 #if str($bmc.motifs) == "yes": 148 --probshared $mpc.probshared
77 --num_motifs $bmc.num_motifs 149 #if str($bmc.nomotifs) == "yes":
78 --mememinw $bmc.min_motif_width 150 --memenmotifs $bmc.memenmotifs
79 --mememaxw $bmc.max_motif_width 151 --mememinw $bmc.mememinw
152 --mememaxw $bmc.mememaxw
80 #else: 153 #else:
81 #set mfoc = $bmc.motif_finding_only_cond 154 --nomotifs
82 --motif_finding_only $mfoc.motif_finding_only 155 #set mfoc = $bmc.nomotifprior_cond
83 #if str($mfoc.motif_finding_only) == "yes": 156 --nomotifprior $mfoc.nomotifprior
84 --num_motifs $mfoc.num_motifs 157 #if str($mfoc.nomotifprior) == "yes":
85 --mememinw $mfoc.min_motif_width 158 --memenmotifs $mfoc.memenmotifs
86 --mememaxw $mfoc.max_motif_width 159 --mememinw $mfoc.mememinw
160 --mememaxw $mfoc.mememaxw
87 #end if 161 #end if
88 #end if 162 #end if
89 #end if 163 #end if
90 #end if 164 #end if
91 --max_training_rounds $aoc.max_training_rounds 165 ############################
92 --exclude_file $aoc.exclude_file 166 ## Reporting binding events
93 --binding_model_updates $aoc.binding_model_updates 167 ############################
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": 168 #if str($rbec.report_binding_events) == "yes":
112 --minqvalue $rbec.minqvalue 169 --q $rbec.minqvalue
113 --minfold $rbec.minfold 170 --minfold $rbec.minfold
114 --diff_enrichment_tests $rbec.diff_enrichment_tests 171 #if str($rbec.nodifftests) == "no":
172 --nodifftests
173 #end if
115 --edgerod $rbec.edgerod 174 --edgerod $rbec.edgerod
116 --diffp $rbec.diffp 175 --diffp $rbec.diffp
117 #end if 176 #end if
118 #if str($sdc.scale_data) == "yes":
119 --noscaling $sdc.scaling
120 --medianscale $sdc.medianscale
121 --sesscale $sdc.sesscale
122 --scalewin $sdc.scalewin
123 #end if
124 #end if 177 #end if
125 --output_html_path "$output_html" 178 --out "$output_html.files_path"
126 --output_html_files_path "$output_html.files_path" 179 > "$output_html"
127 #if str($output_process_log) == "yes": 180 ##if str($output_process_log) == "yes":
128 --output_process_path "$output_process" 181 ## --output_process_path "$output_process"
129 #end if 182 ###end if
130 ]]> 183 ]]>
131 </command> 184 </command>
132 <inputs> 185 <inputs>
133 <repeat name="input_items" title="Input files, attributes and options" min="1"> 186 <param name="input" type="data" format="bam,bed,scidx" label="Add input file" help="Supported formats are bam, bed and scidx">
134 <param name="input" type="data" format="bam,bed,scidx" label="Add input file" help="Supported formats are bam, bed and scidx"> 187 <validator type="unspecified_build" />
135 <validator type="unspecified_build" /> 188 </param>
136 </param> 189 <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag">
137 <conditional name="signal_control_cond"> 190 <option value="no" selected="True">No</option>
138 <param name="signal_control" type="select" label="Is this experiment signal or control?"> 191 <option value="yes">Yes</option>
139 <option value="Signal" selected="True">Signal</option> 192 </param>
140 <option value="Control">Control</option> 193 <!--
141 </param> 194 ############################
142 <when value="Signal"> 195 ## Advanced options
143 <param name="replicate_name" type="text" label="Replicate name" /> 196 ############################
144 <expand macro="rd_cond" /> 197 -->
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"> 198 <conditional name="advanced_options_cond">
165 <param name="advanced_options" type="select" label="Advanced options"> 199 <param name="advanced_options" type="select" label="Advanced options">
166 <option value="hide" selected="true">Hide</option> 200 <option value="hide" selected="true">Hide</option>
167 <option value="display">Display</option> 201 <option value="display">Display</option>
168 </param> 202 </param>
169 <when value="display"> 203 <when value="display">
204 <!--
205 ############################
206 ## Limits on how many reads
207 ############################
208 -->
209 <conditional name="reads_limits_options_cond">
210 <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.">
211 <option value="no" selected="True">No</option>
212 <option value="yes">Yes</option>
213 </param>
214 <when value="no" />
215 <when value="yes">
216 <param name="fixedpb" type="integer" value="0" min="0" label="Fixed per-base limit" help="Zero value estimates from background model"/>
217 <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" />
218 <param name="nonunique" type="select" label="Use non-unique reads?">
219 <option value="no" selected="True">No</option>
220 <option value="yes">Yes</option>
221 </param>
222 <param name="mappability" type="float" value="0.0" min="0.8" label="Fraction of the genome that is mappable for these experiments" />
223 <param name="nocache" type="select" label="Turn off caching of the entire set of experiments?" help="Run slower with less memory" >
224 <option value="no" selected="True">No</option>
225 <option value="yes">Yes</option>
226 </param>
227 </when>
228 </conditional>
229 <!--
230 ############################
231 ## Scaling data
232 ############################
233 -->
234 <conditional name="scale_data_cond">
235 <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.">
236 <option value="no" selected="True">No</option>
237 <option value="yes">Yes</option>
238 </param>
239 <when value="yes">
240 <param name="scaling" type="select" label="Use signal vs control scaling?">
241 <option value="yes" selected="True">Yes</option>
242 <option value="no">No</option>
243 </param>
244 <param name="medianscale" type="select" label="Use the median signal/control ratio as the scaling factor?">
245 <option value="no" selected="True">No</option>
246 <option value="yes">Yes</option>
247 </param>
248 <param name="regressionscale" type="select" label="Use scaling by regression on binned tag counts?">
249 <option value="no" selected="True">No</option>
250 <option value="yes">Yes</option>
251 </param>
252 <param name="sesscale" type="select" label="Estimate scaling factor by SES?" help="SES: Diaz, et al. Stat Appl Genet Mol Biol. 2012">
253 <option value="no" selected="True">No</option>
254 <option value="yes">Yes</option>
255 </param>
256 <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" />
257 <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)." />
258 <param name="plotscaling" type="select" label="Plot diagnostic information for the chosen scaling method?">
259 <option value="no" selected="True">No</option>
260 <option value="yes">Yes</option>
261 </param>
262 </when>
263 <when value="no" />
264 </conditional>
265 <!--
266 ############################
267 ## Running MultiGPS
268 ############################
269 -->
270 <param name="nomodelupdate" type="select" label="Perform binding model updates?">
271 <option value="yes" selected="True">Yes</option>
272 <option value="no">No</option>
273 </param>
274 <param name="minmodelupdateevents" type="integer" value="500" min="0" label="Minimum number of events to support an update of the read distribution" />
275 <param name="nomodelsmoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline.">
276 <option value="yes" selected="True">Yes</option>
277 <option value="no">No</option>
278 </param>
279 <param name="splinesmoothparam" type="integer" value="30" min="0" label="Spline smoothing parameter" />
280 <conditional name="gauss_model_smoothing_cond">
281 <param name="gaussmodelsmoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline.">
282 <option value="no" selected="True">No</option>
283 <option value="yes">Yes</option>
284 </param>
285 <when value="no" />
286 <when value="yes">
287 <param name="gausssmoothparam" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." />
288 </when>
289 </conditional>
290 <param name="jointinmodel" type="select" label="Allow joint events in model updates?">
291 <option value="no" selected="True">No</option>
292 <option value="yes">Yes</option>
293 </param>
294 <param name="fixedmodelrange" type="select" label="Keep binding model range fixed to inital size?" help="Select No to vary automatically">
295 <option value="no" selected="True">No</option>
296 <option value="yes">Yes</option>
297 </param>
298 <param name="prlogconf" type="integer" value="-6" label="Poisson log threshold for potential region scanning" />
299 <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." />
300 <param name="alphascale" type="float" value="1.0" min="0" label="Alpha scaling factor" />
301 <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.">
302 <option value="yes" selected="True">Yes</option>
303 <option value="no">No</option>
304 </param>
305 <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." />
306 <!--
307 ############################
308 ## MultiGPS priors
309 ############################
310 -->
170 <conditional name="use_motif_cond"> 311 <conditional name="use_motif_cond">
171 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?"> 312 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
172 <option value="no" selected="True">No</option> 313 <option value="no" selected="True">No</option>
173 <option value="yes">Yes</option> 314 <option value="yes">Yes</option>
174 </param> 315 </param>
175 <when value="yes"> 316 <when value="yes">
317 <!--
318 ############################
319 ## Specifying the genome
320 ############################
321 -->
176 <conditional name="reference_genome_cond"> 322 <conditional name="reference_genome_cond">
177 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome"> 323 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
178 <option value="cached">Locally Cached</option> 324 <option value="cached">locally cached</option>
179 <option value="history">From History</option> 325 <option value="history">from history</option>
180 </param> 326 </param>
181 <when value="cached"> 327 <when value="cached">
182 <param name="reference_genome" type="select" label="Using reference genome"> 328 <param name="reference_genome" type="select" label="Using reference genome">
183 <options from_data_table="all_fasta"> 329 <options from_data_table="all_fasta">
184 <filter type="data_meta" key="dbkey" ref="input_items.input" column="1"/> 330 <filter type="data_meta" key="dbkey" ref="input" column="1"/>
185 </options> 331 </options>
186 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 332 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
187 </param> 333 </param>
188 </when> 334 </when>
189 <when value="history"> 335 <when value="history">
190 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"> 336 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
191 <options> 337 <options>
192 <filter type="data_meta" key="dbkey" ref="input_items.input"/> 338 <filter type="data_meta" key="dbkey" ref="input"/>
193 </options> 339 </options>
194 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/> 340 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
195 </param> 341 </param>
196 </when> 342 </when>
197 </conditional> 343 </conditional>
344 <!--
345 ############################
346 ## MultiGPS priors options
347 ############################
348 -->
198 <conditional name="multigps_priors_cond"> 349 <conditional name="multigps_priors_cond">
199 <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?"> 350 <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?">
200 <option value="no" selected="True">No</option> 351 <option value="no" selected="True">No</option>
201 <option value="yes">Yes</option> 352 <option value="yes">Yes</option>
202 </param> 353 </param>
203 <when value="no" /> 354 <when value="no" />
204 <when value="yes"> 355 <when value="yes">
205 <param name="positional_prior" type="select" label="Perform inter-experiment positional prior?"> 356 <param name="noposprior" type="select" label="Perform inter-experiment positional prior?">
206 <option value="yes" selected="True">Yes</option> 357 <option value="yes" selected="True">Yes</option>
207 <option value="no">No</option> 358 <option value="no">No</option>
208 </param> 359 </param>
209 <param name="events_shared_probability" type="float" value="0.9" min="0.0" label="Probability that events are shared across conditions" /> 360 <param name="probshared" type="float" value="0.9" min="0.0" label="Probability that events are shared across conditions" />
210 <conditional name="both_motifs_cond"> 361 <conditional name="both_motifs_cond">
211 <param name="motifs" type="select" label="Perform both motif-finding and motif priors?"> 362 <param name="nomotifs" type="select" label="Perform both motif-finding and motif priors?">
212 <option value="yes" selected="True">Yes</option> 363 <option value="yes" selected="True">Yes</option>
213 <option value="no">No</option> 364 <option value="no">No</option>
214 </param> 365 </param>
215 <when value="yes"> 366 <when value="yes">
216 <expand macro="motif_finding_params" /> 367 <expand macro="motif_finding_params" />
217 </when> 368 </when>
218 <when value="no"> 369 <when value="no">
219 <conditional name="motif_finding_only_cond"> 370 <conditional name="nomotifprior_cond">
220 <param name="motif_finding_only" type="select" label="Perform motif-finding only?" help="Selecting Yes turns off motif priors."> 371 <param name="nomotifprior" type="select" label="Perform motif-finding only?" help="Selecting Yes turns off motif priors.">
221 <option value="no" selected="True">No</option> 372 <option value="no" selected="True">No</option>
222 <option value="yes">Yes</option> 373 <option value="yes">Yes</option>
223 </param> 374 </param>
224 <when value="no" /> 375 <when value="no" />
225 <when value="yes"> 376 <when value="yes">
231 </when> 382 </when>
232 </conditional> 383 </conditional>
233 </when> 384 </when>
234 <when value="no" /> 385 <when value="no" />
235 </conditional> 386 </conditional>
236 <param name="max_training_rounds" type="integer" value="3" min="0" label="Maximum number of training rounds for updating binding event read distributions" /> 387 <!--
237 <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." /> 388 ############################
238 <param name="binding_model_updates" type="select" label="Perform binding model updates?"> 389 ## Reporting binding events
239 <option value="yes" selected="True">Yes</option> 390 ############################
240 <option value="no">No</option> 391 -->
241 </param>
242 <param name="minmodelupdateevents" type="integer" value="0" min="0" label="Minimum number of events to support an update of the read distribution" />
243 <conditional name="binding_model_smoothing_cond">
244 <param name="binding_model_smoothing" type="select" label="Perform binding model smoothing?" help="Smoothing performed with a cubic spline.">
245 <option value="yes" selected="True">Yes</option>
246 <option value="no">No</option>
247 </param>
248 <when value="yes">
249 <param name="spline_smooth" type="integer" value="0" min="0" label="Smoothing factor" />
250 </when>
251 <when value="no">
252 <conditional name="gauss_model_smoothing_cond">
253 <param name="gauss_model_smoothing" type="select" label="Use Gaussian model smoothing?" help="Select No to smooth with a cubic spline.">
254 <option value="no" selected="True">No</option>
255 <option value="yes">Yes</option>
256 </param>
257 <when value="yes">
258 <param name="gauss_smooth" type="integer" value="3" min="0" label="Smoothing factor" help="Gaussian smoothing standard deviation." />
259 </when>
260 <when value="no" />
261 </conditional>
262 </when>
263 </conditional>
264 <param name="joint_in_model" type="select" label="Allow joint events in model updates?">
265 <option value="no" selected="True">No</option>
266 <option value="yes">Yes</option>
267 </param>
268 <param name="ml_config_not_shared" type="select" label="Share component configs in the ML step?">
269 <option value="yes" selected="True">Yes</option>
270 <option value="no">No</option>
271 </param>
272 <conditional name="reads_limits_options_cond">
273 <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.">
274 <option value="no" selected="True">No</option>
275 <option value="yes">Yes</option>
276 </param>
277 <when value="no" />
278 <when value="yes">
279 <param name="fixedpb" type="integer" value="0" min="0" label="Fixed per-base limit" />
280 <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" />
281 <param name="non_unique_reads" type="select" label="Use non-unique reads">
282 <option value="no" selected="True">No</option>
283 <option value="yes">Yes</option>
284 </param>
285 </when>
286 </conditional>
287 <conditional name="scale_data_cond">
288 <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.">
289 <option value="no" selected="True">No</option>
290 <option value="yes">Yes</option>
291 </param>
292 <when value="yes">
293 <param name="scaling" type="select" label="Use signal vs control scaling?">
294 <option value="yes" selected="True">Yes</option>
295 <option value="no">No</option>
296 </param>
297 <param name="medianscale" type="select" label="Use the median signal/control ratio as the scaling factor?">
298 <option value="yes" selected="True">Yes</option>
299 <option value="no">No</option>
300 </param>
301 <param name="sesscale" type="select" label="Estimate scaling factor by SES?" help="SES: Diaz, et al. Stat Appl Genet Mol Biol. 2012">
302 <option value="yes" selected="True">Yes</option>
303 <option value="no">No</option>
304 </param>
305 <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)." />
306 </when>
307 <when value="no" />
308 </conditional>
309 <conditional name="report_binding_events_cond"> 392 <conditional name="report_binding_events_cond">
310 <param name="report_binding_events" type="select" label="Report binding events?"> 393 <param name="report_binding_events" type="select" label="Report binding events?">
311 <option value="no" selected="True">No</option> 394 <option value="no" selected="True">No</option>
312 <option value="yes">Yes</option> 395 <option value="yes">Yes</option>
313 </param> 396 </param>
314 <when value="no" /> 397 <when value="no" />
315 <when value="yes"> 398 <when value="yes">
316 <param name="minqvalue" type="integer" min="0" value="0" label="Minimum Q-value (corrected p-value) of reported binding events" /> 399 <param name="minqvalue" type="float" min="0" value="0.001" label="Minimum Q-value (corrected p-value) of reported binding events" />
317 <param name="minfold" type="integer" min="0" value="0" label="Minimum event fold-change vs scaled control" /> 400 <param name="minfold" type="float" min="0" value="1.5" label="Minimum event fold-change vs scaled control" />
318 <param name="diff_enrichment_tests" type="select" label="Run differential enrichment tests?"> 401 <param name="nodifftests" type="select" label="Run differential enrichment tests?">
319 <option value="yes" selected="True">Yes</option> 402 <option value="yes" selected="True">Yes</option>
320 <option value="no">No</option> 403 <option value="no">No</option>
321 </param> 404 </param>
322 <param name="edgerod" type="integer" min="0" value="0" label="EdgeR over-dispersion parameter value" /> 405 <param name="edgerod" type="float" min="0" value="0.15" label="EdgeR over-dispersion parameter value" />
323 <param name="diffp" type="integer" min="0" value="0" label="Minimum p-value for reporting differential enrichment" /> 406 <param name="diffp" type="float" min="0" value="0.01" label="Minimum p-value for reporting differential enrichment" />
324 </when> 407 </when>
325 </conditional> 408 </conditional>
326 </when> 409 </when>
327 <when value="hide"/> 410 <when value="hide"/>
328 </conditional> 411 </conditional>
412 <!--
329 <param name="output_process_log" type="select" label="Output MultiGPS process log?"> 413 <param name="output_process_log" type="select" label="Output MultiGPS process log?">
330 <option value="no" selected="True">No</option> 414 <option value="no" selected="True">No</option>
331 <option value="yes">Yes</option> 415 <option value="yes">Yes</option>
332 </param> 416 </param>
417 -->
333 </inputs> 418 </inputs>
334 <outputs> 419 <outputs>
420 <!--
335 <data name="output_process" format="txt" label="${tool.name} on ${on_string} (process log)"> 421 <data name="output_process" format="txt" label="${tool.name} on ${on_string} (process log)">
336 <filter>output_process_log == "yes"</filter> 422 <filter>output_process_log == "yes"</filter>
337 </data> 423 </data>
424 -->
338 <data name="output_html" format="html"/> 425 <data name="output_html" format="html"/>
339 </outputs> 426 </outputs>
340 <tests> 427 <tests>
341 <test> 428 <test>
342 <repeat name="input_items"> 429 <param name="input" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/>
343 <param name="input" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/>
344 <param name="signal_control" value="Signal"/>
345 <param name="condition_name" value="Abf1"/>
346 <param name="replicate_name" value="1"/>
347 <param name="read_distribution" value="no"/>
348 <param name="fixed_read_count" value="no"/>
349 </repeat>
350 <param name="binding_model_smoothing" value="no"/> 430 <param name="binding_model_smoothing" value="no"/>
351 <param name="gauss_model_smoothing" value="yes"/> 431 <param name="gaussmodelsmoothing" value="yes"/>
352 <param name="gauss_smooth" value="3"/> 432 <param name="gausssmoothparam" value="3"/>
353 <param name="use_motif" value="yes"/> 433 <param name="use_motif" value="yes"/>
354 <param name="reference_genome_source" value="history"/> 434 <param name="reference_genome_source" value="history"/>
355 <param name="reference_genome" value="phiX.fasta" dbkey="phiX"/> 435 <param name="reference_genome" value="phiX.fasta" dbkey="phiX"/>
356 <param name="num_motifs" value="3"/> 436 <param name="memenmotifs" value="3"/>
357 <param name="min_motif_width" value="6"/> 437 <param name="mememinw" value="6"/>
358 <param name="max_motif_width" value="16"/> 438 <param name="mememaxw" value="16"/>
359 <param name="output_process_log" value="yes"/> 439 <param name="output_process_log" value="yes"/>
360 <output name="output_process" file="output_process1.txt" ftype="txt" lines_diff="12"/> 440 <output name="output_process" file="output_process1.txt" ftype="txt" lines_diff="12"/>
361 <output name="output_html" file="output_html1.html" ftype="html" lines_diff="12"/> 441 <output name="output_html" file="output_html1.html" ftype="html" lines_diff="12"/>
362 </test> 442 </test>
363 </tests> 443 </tests>