Mercurial > repos > iuc > multigps

comparison multigps.xml @ 2:91127c200437 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iuc
date Mon, 03 Apr 2017 11:21:10 -0400
parents 944dcc240ab2
children d78ff3764fe5
comparison
equal deleted inserted replaced
1:944dcc240ab2 2:91127c200437
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 <requirements>
7 <requirement type="package" version="0.73">multigps</requirement> 7 <requirement type="package" version="0.74">multigps</requirement>
8 </requirements> 8 </requirements>
9 <command detect_errors="aggressive"> 9 <command detect_errors="aggressive">
10 <![CDATA[ 10 <![CDATA[
11 #set output_dir = $output_html.files_path 11 python $__tool_directory__/multigps.py
12 mkdir -p $output_dir &&
13 multigps
14 ## General options 12 ## General options
13 #set single_or_multi_expt = $single_or_multi_expt_cond.single_or_multi_expt
14 #if str($single_or_multi_expt) == 'multi':
15 #for $i in $single_or_multi_expt_cond['input_items']:
16 #set file_name = $i['input']
17 #set label_cond = $i['label_cond']
18 #set label = $label_cond.label
19 #set file_format = $i['input'].ext
20 #set condition_name = $i['condition_name']
21 #set replicate_name = 'None'
22 #set experiment_type = $i['experiment_type']
23 #set fixed_read_count = $i['fixedreadcount']
24 #if str($label) == 'Signal':
25 #set replicate_name = $label_cond['replicate_name']
26 #else if str($label) == 'Control':
27 #set rncond = $label_cond['replicate_name_cond']
28 #if str($rncond['specify_replicate_name']) == 'yes':
29 #set replicate_name = $rncond['replicate_name']
30 #end if
31 #end if
32 --input_item '$file_name' '$label' '$file_format' '$condition_name' '$replicate_name' '$experiment_type' '$fixed_read_count'
33 #end for
34 #else:
35 #set expt = $single_or_multi_expt_cond.expt
36 #set control = $single_or_multi_expt_cond.control
37 --expt '$expt'
38 --format $expt.ext
39 #if str($control) != 'None':
40 --control '$control'
41 #end if
42 #end if
15 ## Append .txt extensions to events hrefs 43 ## Append .txt extensions to events hrefs
16 ## in output dataset so files will render 44 ## in output dataset so files will render
17 ## in the browser. 45 ## in the browser.
18 --eventsaretxt 46 --eventsaretxt 'true'
19 ## Do not run the parallel version of meme 47 ## Do not run the parallel version of meme.
20 ## since it is not yet available in conda. 48 --meme1proc 'true'
21 --meme1proc
22 --expt '$expt'
23 --format $expt.ext
24 #if str($ctrl) != 'None':
25 --ctrl '$ctrl'
26 #end if
27 --threads \${GALAXY_SLOTS:-4} 49 --threads \${GALAXY_SLOTS:-4}
28 --geninfo '$chromInfo' 50 --chrom_len_file '$chromInfo'
29 ## Advanced options 51 ## Advanced options
30 #set aoc = $advanced_options_cond 52 #set aoc = $advanced_options_cond
31 #if str($aoc.advanced_options) == 'display': 53 #if str($aoc.advanced_options) == 'display':
32 #set bmsc = $aoc.binding_model_smoothing_cond 54 #set bmsc = $aoc.binding_model_smoothing_cond
33 #set gmsc = $aoc.gauss_model_smoothing_cond 55 #set gmsc = $aoc.gauss_model_smoothing_cond
37 #set umc = $aoc.use_motif_cond 59 #set umc = $aoc.use_motif_cond
38 #if str($umc.use_motif) == 'yes': 60 #if str($umc.use_motif) == 'yes':
39 #set rgc = $umc.reference_genome_cond 61 #set rgc = $umc.reference_genome_cond
40 --seq 62 --seq
41 #if str($rgc.reference_genome_source) == 'cached': 63 #if str($rgc.reference_genome_source) == 'cached':
42 '${rgc.reference_genome.fields.path}' 64 '${rgc.reference_genome.fields.path}'
43 #else: 65 #else:
44 '${rgc.reference_genome}' 66 '${rgc.reference_genome}'
45 #end if 67 #end if
46 #end if 68 #end if
47 ## Limits on how many reads 69 ## Limits on how many reads
48 #if str($rloc.reads_limits) == 'yes': 70 #if str($rloc.reads_limits) == 'yes':
49 --fixedpb $rloc.fixedpb 71 --fixedpb $rloc.fixedpb
50 --poissongausspb $rloc.poissongausspb 72 --poissongausspb $rloc.poissongausspb
51 #if str($rloc.nonunique) == 'yes': 73 #if str($rloc.nonunique) == 'yes':
52 --nonunique 74 --nonunique 'true'
53 #end if 75 #end if
54 --mappability $rloc.mappability 76 --mappability $rloc.mappability
55 #if str($rloc.nocache) == 'yes': 77 #if str($rloc.nocache) == 'yes':
56 --nocache 78 --nocache 'true'
57 #end if 79 #end if
58 #end if 80 #end if
59 ## Scaling data 81 ## Scaling data
60 #if str($sdc.scale_data) == 'yes': 82 #if str($sdc.scale_data) == 'yes':
61 #if str($sdc.scaling) == 'no': 83 #if str($sdc.scaling) == 'no':
78 --plotscaling $sdc.plotscaling 100 --plotscaling $sdc.plotscaling
79 #end if 101 #end if
80 #end if 102 #end if
81 ## Running MultiGPS 103 ## Running MultiGPS
82 #if str($aoc.readdistributionfile) != 'None': 104 #if str($aoc.readdistributionfile) != 'None':
83 --d '$aoc.readdistributionfile' 105 --readdistributionfile '$aoc.readdistributionfile'
84 #end if 106 #end if
85 --r $aoc.maxtrainingrounds 107 --maxtrainingrounds $aoc.maxtrainingrounds
86 #if str($aoc.nomodelupdate) == 'no': 108 #if str($aoc.nomodelupdate) == 'no':
87 --nomodelupdate 109 --nomodelupdate 'true'
88 #end if 110 #end if
89 --minmodelupdateevents $aoc.minmodelupdateevents 111 --minmodelupdateevents $aoc.minmodelupdateevents
90 #if str($bmsc.nomodelsmoothing) == 'no': 112 #if str($bmsc.nomodelsmoothing) == 'no':
91 --nomodelsmoothing 113 --nomodelsmoothing 'true'
92 #else: 114 #else:
93 --splinesmoothparam $bmsc.splinesmoothparam 115 --splinesmoothparam $bmsc.splinesmoothparam
94 #end if 116 #end if
95 #if str($gmsc.gaussmodelsmoothing) == 'yes': 117 #if str($gmsc.gaussmodelsmoothing) == 'yes':
96 --gaussmodelsmoothing 118 --gaussmodelsmoothing 'true'
97 --gausssmoothparam $gmsc.gausssmoothparam 119 --gausssmoothparam $gmsc.gausssmoothparam
98 #end if 120 #end if
99 #if str($aoc.jointinmodel) == 'yes': 121 #if str($aoc.jointinmodel) == 'yes':
100 --jointinmodel 122 --jointinmodel 'true'
101 #end if 123 #end if
102 #if str($aoc.fixedmodelrange) == 'yes': 124 #if str($aoc.fixedmodelrange) == 'yes':
103 --fixedmodelrange 125 --fixedmodelrange 'true'
104 #end if 126 #end if
105 --prlogconf $aoc.prlogconf 127 --prlogconf $aoc.prlogconf
106 #if $aoc.fixedalpha > 0: 128 #if $aoc.fixedalpha > 0:
107 --fixedalpha $aoc.fixedalpha 129 --fixedalpha $aoc.fixedalpha
108 #end if 130 #end if
109 --alphascale $aoc.alphascale 131 --alphascale $aoc.alphascale
110 #if str($aoc.mlconfignotshared) == 'no': 132 #if str($aoc.mlconfignotshared) == 'no':
111 --mlconfignotshared 133 --mlconfignotshared 'true'
112 #end if 134 #end if
113 #if str($aoc.exclude) != 'None': 135 #if str($aoc.exclude) != 'None':
114 --exclude '$aoc.exclude' 136 --exclude '$aoc.exclude'
115 #end if 137 #end if
116 ## MultiGPS priors 138 ## MultiGPS priors
117 #if str($umc.use_motif) == 'yes': 139 #if str($umc.use_motif) == 'yes':
118 #set mpc = $umc.multigps_priors_cond 140 #set mpc = $umc.multigps_priors_cond
119 #if str($mpc.multigps_priors) == 'yes': 141 #if str($mpc.multigps_priors) == 'yes':
120 #set bmc = $mpc.both_motifs_cond 142 #set bmc = $mpc.both_motifs_cond
121 #if str($mpc.noposprior) == 'no': 143 #if str($mpc.noposprior) == 'no':
122 --noposprior 144 --noposprior 'true'
123 #end if 145 #end if
124 --probshared $mpc.probshared 146 --probshared $mpc.probshared
125 #if str($bmc.nomotifs) == 'yes': 147 #if str($bmc.nomotifs) == 'yes':
126 --memenmotifs $bmc.memenmotifs 148 --memenmotifs $bmc.memenmotifs
127 --mememinw $bmc.mememinw 149 --mememinw $bmc.mememinw
128 --mememaxw $bmc.mememaxw 150 --mememaxw $bmc.mememaxw
129 #else: 151 #else:
130 #set mfoc = $bmc.nomotifprior_cond 152 #set nmpc = $bmc.nomotifprior_cond
131 --nomotifs 153 --nomotifs 'true'
132 --nomotifprior $mfoc.nomotifprior 154 #if str($nmpc.nomotifprior) == 'yes':
133 #if str($mfoc.nomotifprior) == 'yes': 155 --nomotifprior 'true'
134 --memenmotifs $mfoc.memenmotifs 156 --memenmotifs $nmpc.memenmotifs
135 --mememinw $mfoc.mememinw 157 --mememinw $nmpc.mememinw
136 --mememaxw $mfoc.mememaxw 158 --mememaxw $nmpc.mememaxw
137 #end if 159 #end if
138 #end if 160 #end if
139 #end if 161 #end if
140 #end if 162 #end if
141 ## Reporting binding events 163 ## Reporting binding events
142 #if str($rbec.report_binding_events) == 'yes': 164 #if str($rbec.report_binding_events) == 'yes':
143 --q $rbec.minqvalue 165 --minqvalue $rbec.minqvalue
144 --minfold $rbec.minfold 166 --minfold $rbec.minfold
145 #if str($rbec.nodifftests) == 'no': 167 #if str($rbec.nodifftests) == 'no':
146 --nodifftests 168 --nodifftests 'true'
147 #end if 169 #end if
148 --edgerod $rbec.edgerod 170 --edgerod $rbec.edgerod
149 --diffp $rbec.diffp 171 --diffp $rbec.diffp
150 #end if 172 #end if
151 #end if 173 #end if
152 2>&1 174 --output_html_files_path '$output_html.files_path'
153 --out '$output_html.files_path' 175 --replicates_counts '$replicates_counts'
154 && cp $output_dir/*.events.txt '$experiment_events' 176 --output_bed '$output_bed'
155 && mv $output_dir/*.html '$output_html' 177 --output_html '$output_html'
156 && mv $output_dir/*.table.txt '$all_events_table' 178 --all_events_table '$all_events_table'
157 && mv $output_dir/*.counts '$replicates_counts'
158 ]]> 179 ]]>
159 </command> 180 </command>
160 <inputs> 181 <inputs>
161 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on"> 182 <conditional name="single_or_multi_expt_cond">
162 <validator type="unspecified_build" /> 183 <param name="single_or_multi_expt" type="select" label="Run MultiGPS on single or multiple inputs?">
163 </param> 184 <option value="multi" selected="True">Multiple inputs</option>
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" /> 185 <option value="single">Single input</option>
186 </param>
187 <when value="multi">
188 <repeat name="input_items" title="Input files, attributes and options" min="2">
189 <param name="input" type="data" format="bam,bed,scidx" label="Run multigps on" help="Supported formats are bam, bed and scidx">
190 <validator type="unspecified_build" />
191 </param>
192 <conditional name="label_cond">
193 <param name="label" type="select" label="This experiment is">
194 <option value="Signal" selected="True">Signal</option>
195 <option value="Control">Control</option>
196 </param>
197 <when value="Signal">
198 <param name="replicate_name" type="text" label="Replicate name" />
199 </when>
200 <when value="Control">
201 <conditional name="replicate_name_cond">
202 <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">
203 <option value="no" selected="True">No</option>
204 <option value="yes">Yes</option>
205 </param>
206 <when value="yes">
207 <param name="replicate_name" type="text" optional="True" label="Replicate name"/>
208 </when>
209 <when value="no" />
210 </conditional>
211 </when>
212 </conditional>
213 <param name="condition_name" type="text" label="Condition name" />
214 <param name="experiment_type" type="select" label="Experiment type for this replicate">
215 <option value="None" selected="True">Do not set</option>
216 <option value="chipseq">ChIP-seq</option>
217 <option value="chipexo">ChIP-exo</option>
218 </param>
219 <param name="fixedreadcount" type="select" label="Use fixed per-base read count limit for this replicate?" help="Selecting No uses a global per-base limit that is estimated from a Poisson distribution.">
220 <option value="None" selected="True">No</option>
221 <option value="P">Yes</option>
222 </param>
223 </repeat>
224 </when>
225 <when value="single">
226 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
227 <validator type="unspecified_build" />
228 </param>
229 <param name="control" 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" />
230 </when>
231 </conditional>
165 <!-- Advanced options --> 232 <!-- Advanced options -->
166 <conditional name="advanced_options_cond"> 233 <conditional name="advanced_options_cond">
167 <param name="advanced_options" type="select" label="Advanced options"> 234 <param name="advanced_options" type="select" label="Advanced options">
168 <option value="hide" selected="true">Hide</option> 235 <option value="hide" selected="true">Hide</option>
169 <option value="display">Display</option> 236 <option value="display">Display</option>
280 <option value="history">from history</option> 347 <option value="history">from history</option>
281 </param> 348 </param>
282 <when value="cached"> 349 <when value="cached">
283 <param name="reference_genome" type="select" label="Using reference genome"> 350 <param name="reference_genome" type="select" label="Using reference genome">
284 <options from_data_table="all_fasta"> 351 <options from_data_table="all_fasta">
285 <filter type="data_meta" key="dbkey" ref="expt" column="1"/> 352 <!-- <filter type="data_meta" key="dbkey" ref="expt" column="1"/> does not yet work in a repeat...-->
286 </options> 353 </options>
287 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 354 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
288 </param> 355 </param>
289 </when> 356 </when>
290 <when value="history"> 357 <when value="history">
291 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"> 358 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
292 <options> 359 <options>
293 <filter type="data_meta" key="dbkey" ref="expt"/> 360 <!-- <filter type="data_meta" key="dbkey" ref="expt"/> does not yet work in a repeat...-->
294 </options> 361 </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"/> 362 <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> 363 </param>
297 </when> 364 </when>
298 </conditional> 365 </conditional>
356 </when> 423 </when>
357 <when value="hide" /> 424 <when value="hide" />
358 </conditional> 425 </conditional>
359 </inputs> 426 </inputs>
360 <outputs> 427 <outputs>
361 <data name="replicates_counts" format="tabular" label="${tool.name} replicates counts on ${on_string}"/> 428 <data name="output_bed" format="bed" label="${tool.name} (bed) on ${on_string}"/>
362 <data name="all_events_table" format="tabular" label="${tool.name} all events table on ${on_string}"/> 429 <data name="output_html" format="html" label="${tool.name} (html) on ${on_string}"/>
363 <data name="experiment_events" format="tabular" label="${tool.name} experiment events on ${on_string}"/> 430 <data name="replicates_counts" format="tabular" label="${tool.name} (replicates counts) on ${on_string}"/>
364 <data name="output_html" format="html" label="${tool.name} on ${on_string}"/> 431 <data name="all_events_table" format="tabular" label="${tool.name} (all events table) on ${on_string}"/>
365 </outputs> 432 </outputs>
366 <tests> 433 <tests>
367 <test> 434 <test>
435 <param name="single_or_multi_expt" value="single" />
368 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" /> 436 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
369 <param name="advanced_options_cond" value="hide" /> 437 <param name="advanced_options" value="hide" />
370 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/> 438 <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"/> 439 <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"/> 440 <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"/> 441 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
374 </test> 442 </test>
375 <test> 443 <test>
444 <param name="single_or_multi_expt" value="single" />
376 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" /> 445 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
377 <param name="ctrl" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" /> 446 <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
378 <param name="advanced_options_cond" value="display" /> 447 <param name="advanced_options" value="display" />
379 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/> 448 <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"/> 449 <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"/> 450 <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"/> 451 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
383 </test> 452 </test>
384 </tests> 453 </tests>
385 <help> 454 <help>