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comparison multigps.xml @ 21:6ded14465b74 draft

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author greg
date Tue, 13 Dec 2016 14:49:54 -0500
parents 0ea6413d66b2
children 2e44fe6a99c7
comparison
equal deleted inserted replaced
20:0ea6413d66b2 21:6ded14465b74
1 <tool id="multigps" name="MultiGPS" version="0.72.0"> 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>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <requirements>
7 <requirement type="package" version="0.72">multigps</requirement>
8 </requirements>
7 <command detect_errors="aggressive"> 9 <command detect_errors="aggressive">
8 <command>
9 <![CDATA[ 10 <![CDATA[
10 multigps 11 multigps
11 ############################ 12 ############################
12 ## General options 13 ## General options
13 ############################ 14 ############################
14 --input "$input" 15 --expt "$expt"
15 --format "$input.ext" 16 --format "$expt.ext"
17 #if len($ctrl) > 0:
18 --ctrl "$ctrl"
19 #end if
16 #if str($verbose) == 'yes': 20 #if str($verbose) == 'yes':
17 --verbose 21 --verbose
18 #end if 22 #end if
19 --threads="\${GALAXY_SLOTS:-4}" 23 --threads="\${GALAXY_SLOTS:-4}"
20 ############################ 24 ############################
21 ## Advanced options 25 ## Advanced options
22 ############################ 26 ############################
23 #set aoc = $advanced_options_cond 27 #set aoc = $advanced_options_cond
24 #if str($aoc.advanced_options) == "display": 28 #if str($aoc.advanced_options) == 'display':
25 #set bmsc = $aoc.binding_model_smoothing_cond 29 #set bmsc = $aoc.binding_model_smoothing_cond
26 #set gmsc = $aoc.gauss_model_smoothing_cond 30 #set gmsc = $aoc.gauss_model_smoothing_cond
27 #set rbec = $aoc.report_binding_events_cond 31 #set rbec = $aoc.report_binding_events_cond
28 #set rloc = $aoc.reads_limits_options_cond 32 #set rloc = $aoc.reads_limits_options_cond
29 #set sdc = $aoc.scale_data_cond 33 #set sdc = $aoc.scale_data_cond
30 #set umc = $aoc.use_motif_cond 34 #set umc = $aoc.use_motif_cond
35 #set mpc = $umc.multigps_priors_cond
36 #set bmc = $mpc.both_motifs_cond
37 #set rgc = $umc.reference_genome_cond
31 ############################ 38 ############################
32 ## Limits on how many reads 39 ## Limits on how many reads
33 ############################ 40 ############################
34 #if str($rloc.reads_limits) == "yes": 41 #if str($rloc.reads_limits) == 'yes':
35 --fixedpb $rloc.fixedpb 42 --fixedpb $rloc.fixedpb
36 --poissongausspb $rloc.poissongausspb 43 --poissongausspb $rloc.poissongausspb
37 #if str($rloc.nonunique) == "yes": 44 #if str($rloc.nonunique) == 'yes':
38 --nonunique 45 --nonunique
39 #end if 46 #end if
40 --mappability $rloc.mappability 47 --mappability $rloc.mappability
41 #end if 48 #end if
42 #if str($rloc.nocache) == "yes": 49 #if str($rloc.nocache) == 'yes':
43 --nocache 50 --nocache
44 #end if 51 #end if
45 ############################ 52 ############################
46 ## Scaling data 53 ## Scaling data
47 ############################ 54 ############################
98 --exclude "$aoc.exclude" 105 --exclude "$aoc.exclude"
99 ############################ 106 ############################
100 ## MultiGPS priors 107 ## MultiGPS priors
101 ############################ 108 ############################
102 #if str($umc.use_motif) == 'yes': 109 #if str($umc.use_motif) == 'yes':
103 #set rgc = $umc.reference_genome_cond
104 #if str($rgc.reference_genome_source) == "cached": 110 #if str($rgc.reference_genome_source) == "cached":
105 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0] 111 #set seq_dir = os.path.split($rgc.reference_genome.fields.path)[0]
106 #else: 112 #else:
107 ## MultiGPS requires a directory containing reference files, so symlink the history dataset. 113 ## MultiGPS requires a directory containing reference files, so symlink the history dataset.
108 #import os 114 #import os
111 #set seq_file = str($rgc.reference_genome) 117 #set seq_file = str($rgc.reference_genome)
112 #set tmp_filename = "%s.fa" % str($rgc.reference_genome.dbkey) 118 #set tmp_filename = "%s.fa" % str($rgc.reference_genome.dbkey)
113 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename) 119 #set tmp_seq_file = os.path.join($seq_dir, $tmp_filename)
114 ln -f -s $tmp_seq_file $seq_file && 120 ln -f -s $tmp_seq_file $seq_file &&
115 #end if 121 #end if
116 #set mpc = $umc.multigps_priors_cond
117 --seq $seq_dir 122 --seq $seq_dir
118 --geninfo ${chromInfo} 123 --geninfo ${chromInfo}
119 #if str($mpc.multigps_priors) == 'yes': 124 #if str($mpc.multigps_priors) == 'yes':
120 #set bmc = $mpc.both_motifs_cond
121 #if str($mpc.noposprior) == 'no': 125 #if str($mpc.noposprior) == 'no':
122 --noposprior 126 --noposprior
123 #end if 127 #end if
124 --probshared $mpc.probshared 128 --probshared $mpc.probshared
125 #if str($bmc.nomotifs) == 'yes': 129 #if str($bmc.nomotifs) == 'yes':
151 --diffp $rbec.diffp 155 --diffp $rbec.diffp
152 #end if 156 #end if
153 #end if 157 #end if
154 --out "$output_html.files_path" 158 --out "$output_html.files_path"
155 > "$output_html" 159 > "$output_html"
156 ##if str($output_process_log) == 'yes':
157 ## --output_process_path "$output_process"
158 ###end if
159 ]]> 160 ]]>
160 </command> 161 </command>
161 <inputs> 162 <inputs>
162 <param name="input" type="data" format="bam,bed,scidx" label="Add input file" help="Supported formats are bam, bed and scidx"> 163 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
163 <validator type="unspecified_build" /> 164 <validator type="unspecified_build" />
164 </param> 165 </param>
166 <param name="ctrl" type="data" format="bam,bed,scidx" optional="True" label="Optional file containing file containing reads from a control experiment" help="Must be same forat as the input above" />
165 <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag"> 167 <param name="verbose" type="select" label="Generate intermediate files and extra output?" help="Verbose flag">
166 <option value="no" selected="True">No</option> 168 <option value="no" selected="True">No</option>
167 <option value="yes">Yes</option> 169 <option value="yes">Yes</option>
168 </param> 170 </param>
169 <!-- 171 <!--
276 <param name="alphascale" type="float" value="1.0" min="0" label="Alpha scaling factor" /> 278 <param name="alphascale" type="float" value="1.0" min="0" label="Alpha scaling factor" />
277 <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."> 279 <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.">
278 <option value="yes" selected="True">Yes</option> 280 <option value="yes" selected="True">Yes</option>
279 <option value="no">No</option> 281 <option value="no">No</option>
280 </param> 282 </param>
281 <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." /> 283 <param name="exclude" type="data" optional="True" format="tabular" 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." />
282 <!-- 284 <!--
283 ############################ 285 ############################
284 ## MultiGPS priors 286 ## MultiGPS priors
285 ############################ 287 ############################
286 --> 288 -->
301 <option value="history">from history</option> 303 <option value="history">from history</option>
302 </param> 304 </param>
303 <when value="cached"> 305 <when value="cached">
304 <param name="reference_genome" type="select" label="Using reference genome"> 306 <param name="reference_genome" type="select" label="Using reference genome">
305 <options from_data_table="all_fasta"> 307 <options from_data_table="all_fasta">
306 <filter type="data_meta" key="dbkey" ref="input" column="1"/> 308 <filter type="data_meta" key="dbkey" ref="expt" column="1"/>
307 </options> 309 </options>
308 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 310 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
309 </param> 311 </param>
310 </when> 312 </when>
311 <when value="history"> 313 <when value="history">
312 <param name="reference_genome" type="data" format="fasta" label="Using reference genome"> 314 <param name="reference_genome" type="data" format="fasta" label="Using reference genome">
313 <options> 315 <options>
314 <filter type="data_meta" key="dbkey" ref="input"/> 316 <filter type="data_meta" key="dbkey" ref="expt"/>
315 </options> 317 </options>
316 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/> 318 <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
317 </param> 319 </param>
318 </when> 320 </when>
319 </conditional> 321 </conditional>
381 <param name="edgerod" type="float" min="0" value="0.15" label="EdgeR over-dispersion parameter value" /> 383 <param name="edgerod" type="float" min="0" value="0.15" label="EdgeR over-dispersion parameter value" />
382 <param name="diffp" type="float" min="0" value="0.01" label="Minimum p-value for reporting differential enrichment" /> 384 <param name="diffp" type="float" min="0" value="0.01" label="Minimum p-value for reporting differential enrichment" />
383 </when> 385 </when>
384 </conditional> 386 </conditional>
385 </when> 387 </when>
386 <when value="hide"/> 388 <when value="hide" />
387 </conditional> 389 </conditional>
388 <!-- 390 <!--
389 <param name="output_process_log" type="select" label="Output MultiGPS process log?"> 391 <param name="output_process_log" type="select" label="Output MultiGPS process log?">
390 <option value="no" selected="True">No</option> 392 <option value="no" selected="True">No</option>
391 <option value="yes">Yes</option> 393 <option value="yes">Yes</option>
392 </param> 394 </param>
393 --> 395 -->
394 </inputs> 396 </inputs>
395 <outputs> 397 <outputs>
396 <!--
397 <data name="output_process" format="txt" label="${tool.name} on ${on_string} (process log)">
398 <filter>output_process_log == "yes"</filter>
399 </data>
400 -->
401 <data name="output_html" format="html"/> 398 <data name="output_html" format="html"/>
402 </outputs> 399 </outputs>
403 <tests> 400 <tests>
404 <test> 401 <test>
405 <param name="input" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/> 402 <param name="expt" value="sacCer3_1.scidx" ftype="scidx" dbkey="sacCer3"/>
406 <param name="binding_model_smoothing" value="no"/> 403 <param name="binding_model_smoothing" value="no"/>
407 <param name="gaussmodelsmoothing" value="yes"/> 404 <param name="gaussmodelsmoothing" value="yes"/>
408 <param name="gausssmoothparam" value="3"/> 405 <param name="gausssmoothparam" value="3"/>
409 <param name="use_motif" value="yes"/> 406 <param name="use_motif" value="yes"/>
410 <param name="reference_genome_source" value="history"/> 407 <param name="reference_genome_source" value="history"/>