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comparison multigps.xml @ 48:6997a4b160c5 draft

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author greg
date Tue, 21 Feb 2017 10:34:57 -0500
parents 7c3ef587aed9
children 20687c85887e
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47:7c3ef587aed9 48:6997a4b160c5
9 <command detect_errors="aggressive"> 9 <command detect_errors="aggressive">
10 <![CDATA[ 10 <![CDATA[
11 #set output_dir = $output_html.files_path 11 #set output_dir = $output_html.files_path
12 mkdir -p $output_dir && 12 mkdir -p $output_dir &&
13 multigps 13 multigps
14 ############################
15 ## General options 14 ## General options
16 ############################
17 ## Append .txt extensions to events hrefs 15 ## Append .txt extensions to events hrefs
18 ## in output dataset so files will render 16 ## in output dataset so files will render
19 ## in the browser. 17 ## in the browser.
20 --eventsaretxt 18 --eventsaretxt
21 ## Do not run the parallel version of meme 19 ## Do not run the parallel version of meme
26 #if str($ctrl) != 'None': 24 #if str($ctrl) != 'None':
27 --ctrl '$ctrl' 25 --ctrl '$ctrl'
28 #end if 26 #end if
29 --threads=\${GALAXY_SLOTS:-4} 27 --threads=\${GALAXY_SLOTS:-4}
30 --geninfo '$chromInfo' 28 --geninfo '$chromInfo'
31 ############################
32 ## Advanced options 29 ## Advanced options
33 ############################
34 #set aoc = $advanced_options_cond 30 #set aoc = $advanced_options_cond
35 #if str($aoc.advanced_options) == 'display': 31 #if str($aoc.advanced_options) == 'display':
36 #set bmsc = $aoc.binding_model_smoothing_cond 32 #set bmsc = $aoc.binding_model_smoothing_cond
37 #set gmsc = $aoc.gauss_model_smoothing_cond 33 #set gmsc = $aoc.gauss_model_smoothing_cond
38 #set rbec = $aoc.report_binding_events_cond 34 #set rbec = $aoc.report_binding_events_cond
46 #else: 42 #else:
47 #set seq = $rgc.reference_genome 43 #set seq = $rgc.reference_genome
48 #end if 44 #end if
49 --seq '$seq' 45 --seq '$seq'
50 #end if 46 #end if
51 ############################
52 ## Limits on how many reads 47 ## Limits on how many reads
53 ############################
54 #if str($rloc.reads_limits) == 'yes': 48 #if str($rloc.reads_limits) == 'yes':
55 --fixedpb $rloc.fixedpb 49 --fixedpb $rloc.fixedpb
56 --poissongausspb $rloc.poissongausspb 50 --poissongausspb $rloc.poissongausspb
57 #if str($rloc.nonunique) == 'yes': 51 #if str($rloc.nonunique) == 'yes':
58 --nonunique 52 --nonunique
60 --mappability $rloc.mappability 54 --mappability $rloc.mappability
61 #if str($rloc.nocache) == 'yes': 55 #if str($rloc.nocache) == 'yes':
62 --nocache 56 --nocache
63 #end if 57 #end if
64 #end if 58 #end if
65 ############################
66 ## Scaling data 59 ## Scaling data
67 ############################
68 #if str($sdc.scale_data) == 'yes': 60 #if str($sdc.scale_data) == 'yes':
69 #if str($sdc.scaling) == 'no': 61 #if str($sdc.scaling) == 'no':
70 --noscaling $sdc.scaling 62 --noscaling $sdc.scaling
71 #end if 63 #end if
72 #if str($sdc.medianscale) == 'yes': 64 #if str($sdc.medianscale) == 'yes':
84 --scalewin $sdc.scalewin 76 --scalewin $sdc.scalewin
85 #if str($sdc.plotscaling) == 'yes': 77 #if str($sdc.plotscaling) == 'yes':
86 --plotscaling $sdc.plotscaling 78 --plotscaling $sdc.plotscaling
87 #end if 79 #end if
88 #end if 80 #end if
89 ############################
90 ## Running MultiGPS 81 ## Running MultiGPS
91 ############################
92 #if str($aoc.readdistributionfile) != 'None': 82 #if str($aoc.readdistributionfile) != 'None':
93 --d '$aoc.readdistributionfile' 83 --d '$aoc.readdistributionfile'
94 #end if 84 #end if
95 --r $aoc.maxtrainingrounds 85 --r $aoc.maxtrainingrounds
96 #if str($aoc.nomodelupdate) == 'no': 86 #if str($aoc.nomodelupdate) == 'no':
121 --mlconfignotshared 111 --mlconfignotshared
122 #end if 112 #end if
123 #if str($aoc.exclude) != 'None': 113 #if str($aoc.exclude) != 'None':
124 --exclude '$aoc.exclude' 114 --exclude '$aoc.exclude'
125 #end if 115 #end if
126 ############################
127 ## MultiGPS priors 116 ## MultiGPS priors
128 ############################
129 #if str($umc.use_motif) == 'yes': 117 #if str($umc.use_motif) == 'yes':
130 #set mpc = $umc.multigps_priors_cond 118 #set mpc = $umc.multigps_priors_cond
131 #if str($mpc.multigps_priors) == 'yes': 119 #if str($mpc.multigps_priors) == 'yes':
132 #set bmc = $mpc.both_motifs_cond 120 #set bmc = $mpc.both_motifs_cond
133 #if str($mpc.noposprior) == 'no': 121 #if str($mpc.noposprior) == 'no':
148 --mememaxw $mfoc.mememaxw 136 --mememaxw $mfoc.mememaxw
149 #end if 137 #end if
150 #end if 138 #end if
151 #end if 139 #end if
152 #end if 140 #end if
153 ############################
154 ## Reporting binding events 141 ## Reporting binding events
155 ############################
156 #if str($rbec.report_binding_events) == 'yes': 142 #if str($rbec.report_binding_events) == 'yes':
157 --q $rbec.minqvalue 143 --q $rbec.minqvalue
158 --minfold $rbec.minfold 144 --minfold $rbec.minfold
159 #if str($rbec.nodifftests) == 'no': 145 #if str($rbec.nodifftests) == 'no':
160 --nodifftests 146 --nodifftests
162 --edgerod $rbec.edgerod 148 --edgerod $rbec.edgerod
163 --diffp $rbec.diffp 149 --diffp $rbec.diffp
164 #end if 150 #end if
165 #end if 151 #end if
166 --out '$output_html.files_path' 152 --out '$output_html.files_path'
167 && mv $output_dir/*.html $output_html 153 && mv $output_dir/*.html $output_html || true
168 && mv $output_dir/*.table.txt $all_events_table 154 && mv $output_dir/*.table.txt $all_events_table || true
169 && mv $output_dir/*.counts $replicates_counts 155 && mv $output_dir/*.counts $replicates_counts || true
170 ]]> 156 ]]>
171 </command> 157 </command>
172 <inputs> 158 <inputs>
173 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on"> 159 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
174 <validator type="unspecified_build" /> 160 <validator type="unspecified_build" />
175 </param> 161 </param>
176 <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" /> 162 <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing reads from a control experiment" help="Must be same forat as the input above" />
177 <!-- 163 <!-- Advanced options -->
178 ############################
179 ## Advanced options
180 ############################
181 -->
182 <conditional name="advanced_options_cond"> 164 <conditional name="advanced_options_cond">
183 <param name="advanced_options" type="select" label="Advanced options"> 165 <param name="advanced_options" type="select" label="Advanced options">
184 <option value="hide" selected="true">Hide</option> 166 <option value="hide" selected="true">Hide</option>
185 <option value="display">Display</option> 167 <option value="display">Display</option>
186 </param> 168 </param>
187 <when value="display"> 169 <when value="display">
188 <!-- 170 <!-- Limits on how many reads -->
189 ############################
190 ## Limits on how many reads
191 ############################
192 -->
193 <conditional name="reads_limits_options_cond"> 171 <conditional name="reads_limits_options_cond">
194 <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."> 172 <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.">
195 <option value="no" selected="True">No</option> 173 <option value="no" selected="True">No</option>
196 <option value="yes">Yes</option> 174 <option value="yes">Yes</option>
197 </param> 175 </param>
208 <option value="no" selected="True">No</option> 186 <option value="no" selected="True">No</option>
209 <option value="yes">Yes</option> 187 <option value="yes">Yes</option>
210 </param> 188 </param>
211 </when> 189 </when>
212 </conditional> 190 </conditional>
213 <!-- 191 <!-- Scaling data -->
214 ############################
215 ## Scaling data
216 ############################
217 -->
218 <conditional name="scale_data_cond"> 192 <conditional name="scale_data_cond">
219 <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."> 193 <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.">
220 <option value="no" selected="True">No</option> 194 <option value="no" selected="True">No</option>
221 <option value="yes">Yes</option> 195 <option value="yes">Yes</option>
222 </param> 196 </param>
244 <option value="yes">Yes</option> 218 <option value="yes">Yes</option>
245 </param> 219 </param>
246 </when> 220 </when>
247 <when value="no" /> 221 <when value="no" />
248 </conditional> 222 </conditional>
249 <!-- 223 <!-- Running MultiGPS -->
250 ############################
251 ## Running MultiGPS
252 ############################
253 -->
254 <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." /> 224 <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." />
255 <param name="maxtrainingrounds" type="integer" value="3" min="0" label="Maximum number of training rounds for updating binding event read distributions" /> 225 <param name="maxtrainingrounds" type="integer" value="3" min="0" label="Maximum number of training rounds for updating binding event read distributions" />
256 <param name="nomodelupdate" type="select" label="Perform binding model updates?"> 226 <param name="nomodelupdate" type="select" label="Perform binding model updates?">
257 <option value="yes" selected="True">Yes</option> 227 <option value="yes" selected="True">Yes</option>
258 <option value="no">No</option> 228 <option value="no">No</option>
292 <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."> 262 <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.">
293 <option value="yes" selected="True">Yes</option> 263 <option value="yes" selected="True">Yes</option>
294 <option value="no">No</option> 264 <option value="no">No</option>
295 </param> 265 </param>
296 <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." /> 266 <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." />
297 <!-- 267 <!-- MultiGPS priors -->
298 ############################
299 ## MultiGPS priors
300 ############################
301 -->
302 <conditional name="use_motif_cond"> 268 <conditional name="use_motif_cond">
303 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?"> 269 <param name="use_motif" type="select" label="Perform motif-finding or use a motif-prior?">
304 <option value="no" selected="True">No</option> 270 <option value="no" selected="True">No</option>
305 <option value="yes">Yes</option> 271 <option value="yes">Yes</option>
306 </param> 272 </param>
307 <when value="yes"> 273 <when value="yes">
308 <!-- 274 <!-- Specifying the genome -->
309 ############################
310 ## Specifying the genome
311 ############################
312 -->
313 <conditional name="reference_genome_cond"> 275 <conditional name="reference_genome_cond">
314 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome"> 276 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
315 <option value="cached">locally cached</option> 277 <option value="cached">locally cached</option>
316 <option value="history">from history</option> 278 <option value="history">from history</option>
317 </param> 279 </param>
330 </options> 292 </options>
331 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/> 293 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
332 </param> 294 </param>
333 </when> 295 </when>
334 </conditional> 296 </conditional>
335 <!-- 297 <!-- MultiGPS priors options -->
336 ############################
337 ## MultiGPS priors options
338 ############################
339 -->
340 <conditional name="multigps_priors_cond"> 298 <conditional name="multigps_priors_cond">
341 <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?"> 299 <param name="multigps_priors" type="select" label="Specify MultiGPS priors options?">
342 <option value="no" selected="True">No</option> 300 <option value="no" selected="True">No</option>
343 <option value="yes">Yes</option> 301 <option value="yes">Yes</option>
344 </param> 302 </param>
373 </when> 331 </when>
374 </conditional> 332 </conditional>
375 </when> 333 </when>
376 <when value="no" /> 334 <when value="no" />
377 </conditional> 335 </conditional>
378 <!-- 336 <!-- Reporting binding events -->
379 ############################
380 ## Reporting binding events
381 ############################
382 -->
383 <conditional name="report_binding_events_cond"> 337 <conditional name="report_binding_events_cond">
384 <param name="report_binding_events" type="select" label="Report binding events?"> 338 <param name="report_binding_events" type="select" label="Report binding events?">
385 <option value="no" selected="True">No</option> 339 <option value="no" selected="True">No</option>
386 <option value="yes">Yes</option> 340 <option value="yes">Yes</option>
387 </param> 341 </param>
490 - **Run differential enrichment tests?** - Choose whether to run differential enrichment tests. 444 - **Run differential enrichment tests?** - Choose whether to run differential enrichment tests.
491 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value. 445 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value.
492 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment. 446 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.
493 447
494 </help> 448 </help>
495 <expand macro="citations" /> 449 <citations>
450 <citation type="doi">10.1371/journal.pcbi.1003501</citation>
451 </citations>
496 </tool> 452 </tool>