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"planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b"
author iuc
date Sun, 22 Dec 2019 12:11:33 -0500
parents 7e0a12282c7f
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1:7e0a12282c7f 2:028fafca04fa
1 <tool id="multigps" name="MultiGPS" version="0.73.0"> 1 <tool id="multigps" name="MultiGPS" version="0.74.0">
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>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements" />
7 <requirement type="package" version="0.73">multigps</requirement>
8 </requirements>
9 <command detect_errors="aggressive"> 7 <command detect_errors="aggressive">
10 <![CDATA[ 8 <![CDATA[
11 #set output_dir = $output_html.files_path 9 #set output_dir = $output_html.files_path
12 mkdir -p $output_dir && 10 mkdir -p $output_dir &&
13 multigps 11 multigps
14 ## General options 12 ## General options
13 --design '$build_design_file'
15 ## Append .txt extensions to events hrefs 14 ## Append .txt extensions to events hrefs
16 ## in output dataset so files will render 15 ## in output dataset so files will render
17 ## in the browser. 16 ## in the browser.
18 --eventsaretxt 17 --eventsaretxt
19 ## Do not run the parallel version of meme 18 ## Do not run the parallel version of meme.
20 ## since it is not yet available in conda.
21 --meme1proc 19 --meme1proc
22 --expt '$expt' 20 --threads \${GALAXY_SLOTS:-4}
23 --format $expt.ext 21 #if str($in_test_mode) == "no":
24 #if str($ctrl) != 'None': 22 --geninfo '$chromInfo'
25 --ctrl '$ctrl' 23 #else:
24 --geninfo '$__tool_directory__/tool-data/hg19.len'
26 #end if 25 #end if
27 --threads \${GALAXY_SLOTS:-4}
28 --geninfo '$chromInfo'
29 ## Advanced options 26 ## Advanced options
30 #set aoc = $advanced_options_cond 27 #set aoc = $advanced_options_cond
31 #if str($aoc.advanced_options) == 'display': 28 #if str($aoc.advanced_options) == 'display':
32 #set bmsc = $aoc.binding_model_smoothing_cond 29 #set bmsc = $aoc.binding_model_smoothing_cond
33 #set gmsc = $aoc.gauss_model_smoothing_cond 30 #set gmsc = $aoc.gauss_model_smoothing_cond
37 #set umc = $aoc.use_motif_cond 34 #set umc = $aoc.use_motif_cond
38 #if str($umc.use_motif) == 'yes': 35 #if str($umc.use_motif) == 'yes':
39 #set rgc = $umc.reference_genome_cond 36 #set rgc = $umc.reference_genome_cond
40 --seq 37 --seq
41 #if str($rgc.reference_genome_source) == 'cached': 38 #if str($rgc.reference_genome_source) == 'cached':
42 '${rgc.reference_genome.fields.path}' 39 '${rgc.reference_genome.fields.path}'
43 #else: 40 #else:
44 '${rgc.reference_genome}' 41 '${rgc.reference_genome}'
45 #end if 42 #end if
46 #end if 43 #end if
47 ## Limits on how many reads 44 ## Limits on how many reads
48 #if str($rloc.reads_limits) == 'yes': 45 #if str($rloc.reads_limits) == 'yes':
49 --fixedpb $rloc.fixedpb 46 --fixedpb $rloc.fixedpb
78 --plotscaling $sdc.plotscaling 75 --plotscaling $sdc.plotscaling
79 #end if 76 #end if
80 #end if 77 #end if
81 ## Running MultiGPS 78 ## Running MultiGPS
82 #if str($aoc.readdistributionfile) != 'None': 79 #if str($aoc.readdistributionfile) != 'None':
83 --d '$aoc.readdistributionfile' 80 --readdistributionfile '$aoc.readdistributionfile'
84 #end if 81 #end if
85 --r $aoc.maxtrainingrounds 82 --maxtrainingrounds $aoc.maxtrainingrounds
86 #if str($aoc.nomodelupdate) == 'no': 83 #if str($aoc.nomodelupdate) == 'no':
87 --nomodelupdate 84 --nomodelupdate
88 #end if 85 #end if
89 --minmodelupdateevents $aoc.minmodelupdateevents 86 --minmodelupdateevents $aoc.minmodelupdateevents
90 #if str($bmsc.nomodelsmoothing) == 'no': 87 #if str($bmsc.nomodelsmoothing) == 'no':
125 #if str($bmc.nomotifs) == 'yes': 122 #if str($bmc.nomotifs) == 'yes':
126 --memenmotifs $bmc.memenmotifs 123 --memenmotifs $bmc.memenmotifs
127 --mememinw $bmc.mememinw 124 --mememinw $bmc.mememinw
128 --mememaxw $bmc.mememaxw 125 --mememaxw $bmc.mememaxw
129 #else: 126 #else:
130 #set mfoc = $bmc.nomotifprior_cond 127 #set nmpc = $bmc.nomotifprior_cond
131 --nomotifs 128 --nomotifs
132 --nomotifprior $mfoc.nomotifprior 129 #if str($nmpc.nomotifprior) == 'yes':
133 #if str($mfoc.nomotifprior) == 'yes': 130 --nomotifprior
134 --memenmotifs $mfoc.memenmotifs 131 --memenmotifs $nmpc.memenmotifs
135 --mememinw $mfoc.mememinw 132 --mememinw $nmpc.mememinw
136 --mememaxw $mfoc.mememaxw 133 --mememaxw $nmpc.mememaxw
137 #end if 134 #end if
138 #end if 135 #end if
139 #end if 136 #end if
140 #end if 137 #end if
141 ## Reporting binding events 138 ## Reporting binding events
142 #if str($rbec.report_binding_events) == 'yes': 139 #if str($rbec.report_binding_events) == 'yes':
143 --q $rbec.minqvalue 140 --minqvalue $rbec.minqvalue
144 --minfold $rbec.minfold 141 --minfold $rbec.minfold
145 #if str($rbec.nodifftests) == 'no': 142 #if str($rbec.nodifftests) == 'no':
146 --nodifftests 143 --nodifftests
147 #end if 144 #end if
148 --edgerod $rbec.edgerod 145 --edgerod $rbec.edgerod
149 --diffp $rbec.diffp 146 --diffp $rbec.diffp
150 #end if 147 #end if
151 #end if 148 #end if
152 2>&1 149 2>&1
153 --out '$output_html.files_path' 150 --out '$output_html.files_path'
154 && cp $output_dir/*.events.txt '$experiment_events' 151 #if str($save_design_file) == 'yes':
152 && cp '$build_design_file' '$output_design_file'
153 #end if
154 && mv $output_dir/*.counts '$replicates_counts'
155 && mv $output_dir/*.bed '$output_bed'
155 && mv $output_dir/*.html '$output_html' 156 && mv $output_dir/*.html '$output_html'
156 && mv $output_dir/*.table.txt '$all_events_table' 157 && mv $output_dir/*.table.txt '$all_events_table'
157 && mv $output_dir/*.counts '$replicates_counts'
158 ]]> 158 ]]>
159 </command> 159 </command>
160 <configfiles>
161 <configfile name="build_design_file"><![CDATA[#for $condition_items in $condition_repeat:
162 #for $signal_items in $condition_items.signal_repeat:
163 #if str($signal_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
164 #set $frc = $signal_items.fixedreadcount_cond.fixedreadcount
165 #else:
166 #set $frc = ''
167 #end if
168 ${signal_items.signal} Signal ${signal_items.signal.ext.upper()} ${condition_items.condition_name} ${signal_items.replicate_name} ${condition_items.experiment_type} ${frc}
169 #end for
170 #for $control_items in $condition_items.control_repeat:
171 #if str($control_items.specify_replicate_name_cond.specify_replicate_name) == 'yes':
172 #set $rn = $control_items.specify_replicate_name_cond.replicate_name
173 #else:
174 #set $rn = ''
175 #end if
176 #if str($control_items.fixedreadcount_cond.fixedreadcount_select) == 'yes':
177 #set $frc = $control_items.fixedreadcount_cond.fixedreadcount
178 #else:
179 #set $frc = ''
180 #end if
181 ${control_items.control} Control ${control_items.control.ext.upper()} ${condition_items.condition_name} ${rn} ${condition_items.experiment_type} ${frc}
182 #end for
183 #end for ]]></configfile>
184 </configfiles>
160 <inputs> 185 <inputs>
161 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on"> 186 <repeat name="condition_repeat" title="Condition" min="1">
162 <validator type="unspecified_build" /> 187 <param name="condition_name" type="text" value="cond" label="Condition name">
188 <validator type="empty_field" />
189 </param>
190 <expand macro="param_experiment_type" />
191 <repeat name="signal_repeat" title="Signal" min="1">
192 <param name="signal" type="data" format="bam,bed,scidx" label="Select signal" help="Supported formats are bam, bed and scidx">
193 <validator type="unspecified_build" />
194 </param>
195 <param name="replicate_name" type="text" value="1" label="Replicate name">
196 <validator type="empty_field" />
197 </param>
198 <expand macro="cond_fixedreadcount" />
199 </repeat>
200 <repeat name="control_repeat" title="Control" min="0">
201 <param name="control" type="data" format="bam,bed,scidx" label="Select control" help="Optional, supported formats are bam, bed and scidx">
202 <validator type="unspecified_build" />
203 </param>
204 <conditional name="specify_replicate_name_cond">
205 <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">
206 <option value="no" selected="True">No</option>
207 <option value="yes">Yes</option>
208 </param>
209 <when value="yes">
210 <param name="replicate_name" type="text" optional="true" label="Replicate name"/>
211 </when>
212 <when value="no" />
213 </conditional>
214 <expand macro="cond_fixedreadcount" />
215 </repeat>
216 </repeat>
217 <param name="save_design_file" type="select" display="radio" label="Output design file?">
218 <option value="no" selected="true">No</option>
219 <option value="yes">Yes</option>
163 </param> 220 </param>
164 <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" />
165 <!-- Advanced options --> 221 <!-- Advanced options -->
166 <conditional name="advanced_options_cond"> 222 <conditional name="advanced_options_cond">
167 <param name="advanced_options" type="select" label="Advanced options"> 223 <param name="advanced_options" type="select" label="Advanced options">
168 <option value="hide" selected="true">Hide</option> 224 <option value="hide" selected="true">Hide</option>
169 <option value="display">Display</option> 225 <option value="display">Display</option>
190 </param> 246 </param>
191 </when> 247 </when>
192 </conditional> 248 </conditional>
193 <!-- Scaling data --> 249 <!-- Scaling data -->
194 <conditional name="scale_data_cond"> 250 <conditional name="scale_data_cond">
195 <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."> 251 <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]">
196 <option value="no" selected="True">No</option> 252 <option value="no" selected="True">No</option>
197 <option value="yes">Yes</option> 253 <option value="yes">Yes</option>
198 </param> 254 </param>
199 <when value="yes"> 255 <when value="yes">
200 <param name="scaling" type="select" label="Use signal vs control scaling?"> 256 <param name="scaling" type="select" label="Use signal vs control scaling?">
280 <option value="history">from history</option> 336 <option value="history">from history</option>
281 </param> 337 </param>
282 <when value="cached"> 338 <when value="cached">
283 <param name="reference_genome" type="select" label="Using reference genome"> 339 <param name="reference_genome" type="select" label="Using reference genome">
284 <options from_data_table="all_fasta"> 340 <options from_data_table="all_fasta">
285 <filter type="data_meta" key="dbkey" ref="expt" column="1"/> 341 <!-- <filter type="data_meta" key="dbkey" ref="expt" column="1"/> does not yet work in a repeat...-->
286 </options> 342 </options>
287 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 343 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
288 </param> 344 </param>
289 </when> 345 </when>
290 <when value="history"> 346 <when value="history">
291 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"> 347 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
292 <options> 348 <options>
293 <filter type="data_meta" key="dbkey" ref="expt"/> 349 <!-- <filter type="data_meta" key="dbkey" ref="expt"/> does not yet work in a repeat...-->
294 </options> 350 </options>
295 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/> 351 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
296 </param> 352 </param>
297 </when> 353 </when>
298 </conditional> 354 </conditional>
354 </when> 410 </when>
355 </conditional> 411 </conditional>
356 </when> 412 </when>
357 <when value="hide" /> 413 <when value="hide" />
358 </conditional> 414 </conditional>
415 <!-- Functional testing -->
416 <param name="in_test_mode" type="hidden" value="no" />
359 </inputs> 417 </inputs>
360 <outputs> 418 <outputs>
361 <data name="replicates_counts" format="tabular" label="${tool.name} replicates counts on ${on_string}"/> 419 <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">
362 <data name="all_events_table" format="tabular" label="${tool.name} all events table on ${on_string}"/> 420 <filter>save_design_file == 'yes'</filter>
363 <data name="experiment_events" format="tabular" label="${tool.name} experiment events on ${on_string}"/> 421 </data>
364 <data name="output_html" format="html" label="${tool.name} on ${on_string}"/> 422 <data name="output_bed" format="bed" label="${tool.name} (bed) on ${on_string}"/>
423 <data name="output_html" format="html" label="${tool.name} (html) on ${on_string}"/>
424 <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/>
425 <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/>
365 </outputs> 426 </outputs>
366 <tests> 427 <tests>
367 <test> 428 <test>
368 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" /> 429 <repeat name="condition_repeat">
369 <param name="advanced_options_cond" value="hide" /> 430 <repeat name="signal_repeat">
431 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
432 </repeat>
433 </repeat>
434 <param name="advanced_options" value="hide" />
435 <param name="in_test_mode" value="yes" />
370 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/> 436 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
371 <output name="experiment_events" file="hg19_experiment_events1.tabular" ftype="tabular"/> 437 <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>
372 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/> 438 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
373 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/> 439 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
374 </test> 440 </test>
375 <test> 441 <test>
376 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" /> 442 <repeat name="condition_repeat">
377 <param name="ctrl" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" /> 443 <repeat name="signal_repeat">
378 <param name="advanced_options_cond" value="display" /> 444 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
445 </repeat>
446 <repeat name="control_repeat">
447 <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
448 </repeat>
449 </repeat>
450 <param name="advanced_options" value="display" />
451 <param name="in_test_mode" value="yes" />
379 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/> 452 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
380 <output name="experiment_events" file="hg19_experiment_events2.tabular" ftype="tabular"/> 453 <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>
381 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/> 454 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
382 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/> 455 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
383 </test> 456 </test>
384 </tests> 457 </tests>
385 <help> 458 <help>
397 470
398 **Options** 471 **Options**
399 472
400 * **Loading data:** 473 * **Loading data:**
401 474
402 - **Optional file containing reads from a control experiment** - must be same format as input experiment 475 - **Optional file containing reads from a control experiment** - file containing reads from a control experiment
403 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model). 476 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
404 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be. 477 - **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. 478 - **Use non-unique reads** - Use non-unique reads.
406 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments 479 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments
407 - **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). 480 - **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).
454 </help> 527 </help>
455 <citations> 528 <citations>
456 <citation type="doi">10.1371/journal.pcbi.1003501</citation> 529 <citation type="doi">10.1371/journal.pcbi.1003501</citation>
457 </citations> 530 </citations>
458 </tool> 531 </tool>
532