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comparison multigps.xml @ 3:d78ff3764fe5 draft

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author iuc
date Mon, 03 Apr 2017 13:38:23 -0400
parents 91127c200437
children 0bec3b2df784
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2:91127c200437 3:d78ff3764fe5
11 python $__tool_directory__/multigps.py 11 python $__tool_directory__/multigps.py
12 ## General options 12 ## General options
13 #set single_or_multi_expt = $single_or_multi_expt_cond.single_or_multi_expt 13 #set single_or_multi_expt = $single_or_multi_expt_cond.single_or_multi_expt
14 #if str($single_or_multi_expt) == 'multi': 14 #if str($single_or_multi_expt) == 'multi':
15 #for $i in $single_or_multi_expt_cond['input_items']: 15 #for $i in $single_or_multi_expt_cond['input_items']:
16 #set file_name = $i['input']
17 #set label_cond = $i['label_cond'] 16 #set label_cond = $i['label_cond']
17 #set file_name = $label_cond.input
18 #set label = $label_cond.label 18 #set label = $label_cond.label
19 #set file_format = $i['input'].ext 19 #set file_format = $label_cond.input.ext
20 #set condition_name = $i['condition_name'] 20 #set condition_name = $label_cond.condition_name
21 #set replicate_name = 'None' 21 #set replicate_name = 'None'
22 #set experiment_type = $i['experiment_type'] 22 #set experiment_type = $label_cond.experiment_type
23 #set fixed_read_count = $i['fixedreadcount'] 23 #set fixed_read_count = $label_cond.fixedreadcount
24 #if str($label) == 'Signal': 24 #if str($label) == 'Signal':
25 #set replicate_name = $label_cond['replicate_name'] 25 #set replicate_name = $label_cond.replicate_name
26 #else if str($label) == 'Control': 26 #else if str($label) == 'Control':
27 #set rncond = $label_cond['replicate_name_cond'] 27 #set rncond = $label_cond.replicate_name_cond
28 #if str($rncond['specify_replicate_name']) == 'yes': 28 #if str($rncond.specify_replicate_name) == 'yes':
29 #set replicate_name = $rncond['replicate_name'] 29 #set replicate_name = $rncond.replicate_name
30 #end if 30 #end if
31 #end if 31 #end if
32 --input_item '$file_name' '$label' '$file_format' '$condition_name' '$replicate_name' '$experiment_type' '$fixed_read_count' 32 --input_item '$file_name' '$label' '$file_format' '$condition_name' '$replicate_name' '$experiment_type' '$fixed_read_count'
33 #end for 33 #end for
34 #else: 34 #else:
184 <option value="multi" selected="True">Multiple inputs</option> 184 <option value="multi" selected="True">Multiple inputs</option>
185 <option value="single">Single input</option> 185 <option value="single">Single input</option>
186 </param> 186 </param>
187 <when value="multi"> 187 <when value="multi">
188 <repeat name="input_items" title="Input files, attributes and options" min="2"> 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"> 189 <conditional name="label_cond">
193 <param name="label" type="select" label="This experiment is"> 190 <param name="label" type="select" label="This experiment is">
194 <option value="Signal" selected="True">Signal</option> 191 <option value="Signal" selected="True">Signal</option>
195 <option value="Control">Control</option> 192 <option value="Control">Control</option>
196 </param> 193 </param>
197 <when value="Signal"> 194 <when value="Signal">
195 <expand macro="label_cond_params_start" />
198 <param name="replicate_name" type="text" label="Replicate name" /> 196 <param name="replicate_name" type="text" label="Replicate name" />
197 <expand macro="label_cond_params_end" />
199 </when> 198 </when>
200 <when value="Control"> 199 <when value="Control">
200 <expand macro="label_cond_params_start" />
201 <conditional name="replicate_name_cond"> 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"> 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> 203 <option value="no" selected="True">No</option>
204 <option value="yes">Yes</option> 204 <option value="yes">Yes</option>
205 </param> 205 </param>
206 <when value="yes"> 206 <when value="yes">
207 <param name="replicate_name" type="text" optional="True" label="Replicate name"/> 207 <param name="replicate_name" type="text" optional="True" label="Replicate name"/>
208 </when> 208 </when>
209 <when value="no" /> 209 <when value="no" />
210 </conditional> 210 </conditional>
211 <expand macro="label_cond_params_end" />
211 </when> 212 </when>
212 </conditional> 213 </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> 214 </repeat>
224 </when> 215 </when>
225 <when value="single"> 216 <when value="single">
226 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on"> 217 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
227 <validator type="unspecified_build" /> 218 <validator type="unspecified_build" />