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comparison cwpair2.xml @ 4:9ed566138ecb draft

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author greg
date Sat, 21 Nov 2015 09:01:46 -0500
parents 507521bf124a
children d455f14530dc
comparison
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3:430a5bdc55a3 4:9ed566138ecb
19 #if str($threshold_format_cond.threshold_format) == "absolute_threshold": 19 #if str($threshold_format_cond.threshold_format) == "absolute_threshold":
20 --absolute_threshold $threshold_format_cond.absolute_threshold 20 --absolute_threshold $threshold_format_cond.absolute_threshold
21 #elif str($threshold_format_cond.threshold_format) == "relative_threshold": 21 #elif str($threshold_format_cond.threshold_format) == "relative_threshold":
22 --relative_threshold $threshold_format_cond.relative_threshold 22 --relative_threshold $threshold_format_cond.relative_threshold
23 #end if 23 #end if
24 --output_files $output_files_cond.output_files 24 --output_files $output_files
25 #if str($output_files_cond.output_files) == "all"
26 --plot_format $output_files_cond.plot_format
27 #end if
28 --sort_chromosome $sort_chromosome 25 --sort_chromosome $sort_chromosome
29 --sort_score $sort_score 26 --sort_score $sort_score
30 --statistics_output "$statistics_output" 27 --statistics_output "$statistics_output"
31 ]]> 28 ]]>
32 </command> 29 </command>
51 </when> 48 </when>
52 <when value="absolute_threshold"> 49 <when value="absolute_threshold">
53 <param name="absolute_threshold" type="float" value="0.0" min="0.0" label="Absolute value to filter below" /> 50 <param name="absolute_threshold" type="float" value="0.0" min="0.0" label="Absolute value to filter below" />
54 </when> 51 </when>
55 </conditional> 52 </conditional>
56 <conditional name="output_files_cond"> 53 <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." >
57 <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." > 54 <option value="simple" selected="True">matched pairs only (S)</option>
58 <option value="simple" selected="True">matched pairs only (S)</option> 55 <option value="simple_orphan">matched pairs and orphans only (O,S)</option>
59 <option value="simple_orphan">matched pairs and orphans only (O,S)</option> 56 <option value="simple_orphan_detail">matched pairs, orphans and details only (D,O,S)</option>
60 <option value="simple_orphan_detail">matched pairs, orphans and details only (D,O,S)</option> 57 <option value="all">no restrictions (output everything: C,D,F,O,P,S)</option>
61 <option value="all">no restrictions (output everything: C,D,F,O,P,S)</option> 58 </param>
62 </param>
63 <when value="simple" />
64 <when value="simple_orphan" />
65 <when value="simple_orphan_detail" />
66 <when value="all">
67 <param name="plot_format" type="select" label="Output format for graph">
68 <option value="pdf" selected="True">Pdf</option>
69 <option value="png">Png</option>
70 <option value="svg">Svg</option>
71 </param>
72 </when>
73 </conditional>
74 <param name="sort_chromosome" type="select" label="Sort output by chromosomes in" help="Chromosome strings that are not numeric will not be sorted" > 59 <param name="sort_chromosome" type="select" label="Sort output by chromosomes in" help="Chromosome strings that are not numeric will not be sorted" >
75 <option value="asc" selected="True">ascending order</option> 60 <option value="asc" selected="True">ascending order</option>
76 <option value="desc">descending order</option> 61 <option value="desc">descending order</option>
77 </param> 62 </param>
78 <param name="sort_score" type="select" label="Sort output by score?"> 63 <param name="sort_score" type="select" label="Sort output by score?">
81 <option value="desc">Yes, in descending order</option> 66 <option value="desc">Yes, in descending order</option>
82 </param> 67 </param>
83 </inputs> 68 </inputs>
84 <outputs> 69 <outputs>
85 <collection name="closest_C_pdf" type="list" label="closest C: ${tool.name} on ${on_string}"> 70 <collection name="closest_C_pdf" type="list" label="closest C: ${tool.name} on ${on_string}">
86 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter> 71 <filter>output_files == "all" and method in ["all", "closest"]</filter>
87 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_C" ext="pdf" visible="false" /> 72 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_C" ext="pdf" visible="false" />
88 </collection> 73 </collection>
89 <collection name="closest_C_png" type="list" label="closest C: ${tool.name} on ${on_string}">
90 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter>
91 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_C" ext="png" visible="false" />
92 </collection>
93 <collection name="closest_C_svg" type="list" label="closest C: ${tool.name} on ${on_string}">
94 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter>
95 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_C" ext="svg" visible="false" />
96 </collection>
97 <collection name="largest_C_pdf" type="list" label="largest C: ${tool.name} on ${on_string}"> 74 <collection name="largest_C_pdf" type="list" label="largest C: ${tool.name} on ${on_string}">
98 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter> 75 <filter>output_files == "all" and method in ["all", "largest"]</filter>
99 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_C" ext="pdf" visible="false" /> 76 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_C" ext="pdf" visible="false" />
100 </collection> 77 </collection>
101 <collection name="largest_C_png" type="list" label="largest C: ${tool.name} on ${on_string}">
102 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter>
103 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_C" ext="png" visible="false" />
104 </collection>
105 <collection name="largest_C_svg" type="list" label="largest C: ${tool.name} on ${on_string}">
106 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter>
107 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_C" ext="svg" visible="false" />
108 </collection>
109 <collection name="mode_C_pdf" type="list" label="mode C: ${tool.name} on ${on_string}"> 78 <collection name="mode_C_pdf" type="list" label="mode C: ${tool.name} on ${on_string}">
110 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter> 79 <filter>output_files == "all" and method in ["all", "mode"]</filter>
111 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_C" ext="pdf" visible="false" /> 80 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_C" ext="pdf" visible="false" />
112 </collection> 81 </collection>
113 <collection name="mode_C_png" type="list" label="mode C: ${tool.name} on ${on_string}">
114 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter>
115 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_C" ext="png" visible="false" />
116 </collection>
117 <collection name="mode_C_svg" type="list" label="mode C: ${tool.name} on ${on_string}">
118 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter>
119 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_C" ext="svg" visible="false" />
120 </collection>
121 <collection name="closest_D" type="list" label="closest D: ${tool.name} on ${on_string}"> 82 <collection name="closest_D" type="list" label="closest D: ${tool.name} on ${on_string}">
122 <filter>output_files_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "closest"]</filter> 83 <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "closest"]</filter>
123 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_D" ext="tabular" visible="false" /> 84 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_D" ext="tabular" visible="false" />
124 </collection> 85 </collection>
125 <collection name="largest_D" type="list" label="largest D: ${tool.name} on ${on_string}"> 86 <collection name="largest_D" type="list" label="largest D: ${tool.name} on ${on_string}">
126 <filter>output_files_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "largest"]</filter> 87 <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "largest"]</filter>
127 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_D" ext="tabular" visible="false" /> 88 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_D" ext="tabular" visible="false" />
128 </collection> 89 </collection>
129 <collection name="mode_D" type="list" label="mode D: ${tool.name} on ${on_string}"> 90 <collection name="mode_D" type="list" label="mode D: ${tool.name} on ${on_string}">
130 <filter>output_files_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "mode"]</filter> 91 <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "mode"]</filter>
131 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_D" ext="tabular" visible="false" /> 92 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_D" ext="tabular" visible="false" />
132 </collection> 93 </collection>
133 <collection name="closest_F_pdf" type="list" label="closest F: ${tool.name} on ${on_string}"> 94 <collection name="closest_F_pdf" type="list" label="closest F: ${tool.name} on ${on_string}">
134 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter> 95 <filter>output_files == "all" and method in ["all", "closest"]</filter>
135 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_F" ext="pdf" visible="false" /> 96 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_F" ext="pdf" visible="false" />
136 </collection> 97 </collection>
137 <collection name="closest_F_png" type="list" label="closest F: ${tool.name} on ${on_string}">
138 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter>
139 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_F" ext="png" visible="false" />
140 </collection>
141 <collection name="closest_F_svg" type="list" label="closest F: ${tool.name} on ${on_string}">
142 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter>
143 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_F" ext="svg" visible="false" />
144 </collection>
145 <collection name="largest_F_pdf" type="list" label="largest F: ${tool.name} on ${on_string}"> 98 <collection name="largest_F_pdf" type="list" label="largest F: ${tool.name} on ${on_string}">
146 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter> 99 <filter>output_files == "all" and method in ["all", "largest"]</filter>
147 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_F" ext="pdf" visible="false" /> 100 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_F" ext="pdf" visible="false" />
148 </collection> 101 </collection>
149 <collection name="largest_F_png" type="list" label="largest F: ${tool.name} on ${on_string}">
150 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter>
151 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_F" ext="png" visible="false" />
152 </collection>
153 <collection name="largest_F_svg" type="list" label="largest F: ${tool.name} on ${on_string}">
154 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter>
155 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_F" ext="svg" visible="false" />
156 </collection>
157 <collection name="mode_F_pdf" type="list" label="mode F: ${tool.name} on ${on_string}"> 102 <collection name="mode_F_pdf" type="list" label="mode F: ${tool.name} on ${on_string}">
158 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter> 103 <filter>output_files == "all" and method in ["all", "mode"]</filter>
159 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_F" ext="pdf" visible="false" /> 104 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_F" ext="pdf" visible="false" />
160 </collection> 105 </collection>
161 <collection name="mode_F_png" type="list" label="mode F: ${tool.name} on ${on_string}">
162 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter>
163 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_F" ext="png" visible="false" />
164 </collection>
165 <collection name="mode_F_svg" type="list" label="mode F: ${tool.name} on ${on_string}">
166 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter>
167 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_F" ext="svg" visible="false" />
168 </collection>
169 <collection name="closest_O" type="list" label="closest O: ${tool.name} on ${on_string}"> 106 <collection name="closest_O" type="list" label="closest O: ${tool.name} on ${on_string}">
170 <filter>output_files_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "closest"]</filter> 107 <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "closest"]</filter>
171 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_O" ext="tabular" visible="false" /> 108 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_O" ext="tabular" visible="false" />
172 </collection> 109 </collection>
173 <collection name="largest_O" type="list" label="largest O: ${tool.name} on ${on_string}"> 110 <collection name="largest_O" type="list" label="largest O: ${tool.name} on ${on_string}">
174 <filter>output_files_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "largest"]</filter> 111 <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "largest"]</filter>
175 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_O" ext="tabular" visible="false" /> 112 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_O" ext="tabular" visible="false" />
176 </collection> 113 </collection>
177 <collection name="mode_O" type="list" label="mode O: ${tool.name} on ${on_string}"> 114 <collection name="mode_O" type="list" label="mode O: ${tool.name} on ${on_string}">
178 <filter>output_files_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "mode"]</filter> 115 <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "mode"]</filter>
179 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_O" ext="tabular" visible="false" /> 116 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_O" ext="tabular" visible="false" />
180 </collection> 117 </collection>
181 <collection name="closest_P_pdf" type="list" label="closest P: ${tool.name} on ${on_string}"> 118 <collection name="closest_P_pdf" type="list" label="closest P: ${tool.name} on ${on_string}">
182 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter> 119 <filter>output_files == "all" and method in ["all", "closest"]</filter>
183 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_P" ext="pdf" visible="false" /> 120 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_P" ext="pdf" visible="false" />
184 </collection> 121 </collection>
185 <collection name="closest_P_png" type="list" label="closest P: ${tool.name} on ${on_string}">
186 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter>
187 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_P" ext="png" visible="false" />
188 </collection>
189 <collection name="closest_P_svg" type="list" label="closest P: ${tool.name} on ${on_string}">
190 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter>
191 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_P" ext="svg" visible="false" />
192 </collection>
193 <collection name="largest_P_pdf" type="list" label="largest P: ${tool.name} on ${on_string}"> 122 <collection name="largest_P_pdf" type="list" label="largest P: ${tool.name} on ${on_string}">
194 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter> 123 <filter>output_files == "all" and method in ["all", "largest"]</filter>
195 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_P" ext="pdf" visible="false" /> 124 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_P" ext="pdf" visible="false" />
196 </collection> 125 </collection>
197 <collection name="largest_P_png" type="list" label="largest P: ${tool.name} on ${on_string}">
198 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter>
199 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_P" ext="png" visible="false" />
200 </collection>
201 <collection name="largest_P_svg" type="list" label="largest P: ${tool.name} on ${on_string}">
202 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter>
203 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_P" ext="svg" visible="false" />
204 </collection>
205 <collection name="mode_P_pdf" type="list" label="mode P: ${tool.name} on ${on_string}"> 126 <collection name="mode_P_pdf" type="list" label="mode P: ${tool.name} on ${on_string}">
206 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter> 127 <filter>output_files == "all" and method in ["all", "mode"]</filter>
207 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_P" ext="pdf" visible="false" /> 128 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_P" ext="pdf" visible="false" />
208 </collection>
209 <collection name="mode_P_png" type="list" label="mode P: ${tool.name} on ${on_string}">
210 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter>
211 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_P" ext="png" visible="false" />
212 </collection>
213 <collection name="mode_P_svg" type="list" label="mode P: ${tool.name} on ${on_string}">
214 <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter>
215 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_P" ext="svg" visible="false" />
216 </collection> 129 </collection>
217 <collection name="closest_S" type="list" label="closest S: ${tool.name} on ${on_string}"> 130 <collection name="closest_S" type="list" label="closest S: ${tool.name} on ${on_string}">
218 <filter>method in ["all", "closest"]</filter> 131 <filter>method in ["all", "closest"]</filter>
219 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_S" ext="gff" visible="false" /> 132 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_S" ext="gff" visible="false" />
220 </collection> 133 </collection>
258 <param name="down_distance" value="100" /> 171 <param name="down_distance" value="100" />
259 <param name="binsize" value="1" /> 172 <param name="binsize" value="1" />
260 <param name="threshold_format" value="relative_threshold" /> 173 <param name="threshold_format" value="relative_threshold" />
261 <param name="relative_threshold" value="0.0" /> 174 <param name="relative_threshold" value="0.0" />
262 <param name="output_files" value="all" /> 175 <param name="output_files" value="all" />
263 <param name="plot_format" value="pdf" />
264 <param name="sort_chromosome" value="asc" /> 176 <param name="sort_chromosome" value="asc" />
265 <param name="sort_score" value="no" /> 177 <param name="sort_score" value="no" />
266 <output_collection name="closest_D" type="list"> 178 <output_collection name="closest_D" type="list">
267 <element name="closest_D_data_1_f0u50d100b1" file="closest_d_output2.tabular" ftype="tabular" /> 179 <element name="closest_D_data_1_f0u50d100b1" file="closest_d_output2.tabular" ftype="tabular" />
268 </output_collection> 180 </output_collection>
314 Takes a list of called peaks on both strands and produces a list of matched pairs and a list of unmatched orphans 226 Takes a list of called peaks on both strands and produces a list of matched pairs and a list of unmatched orphans
315 using a specified method for finding matched pairs. Methods for finding matched pairs are mode, closest, largest 227 using a specified method for finding matched pairs. Methods for finding matched pairs are mode, closest, largest
316 or all (where the analysis is run for each method). A statistics dataset is generated and a collection of datasets 228 or all (where the analysis is run for each method). A statistics dataset is generated and a collection of datasets
317 is produced for each method as follows. 229 is produced for each method as follows.
318 230
319 * **closest/largest/mode C** - the stastics graph in a specified format: pdf, png or svg 231 * **closest/largest/mode C** - the stastics graph in pdf format
320 * **closest/largest/mode D** - the details in tabular format 232 * **closest/largest/mode D** - the details in tabular format
321 * **closest/largest/mode F** - the final plots graph in a specified format: pdf, png or svg 233 * **closest/largest/mode F** - the final plots graph in pdf format
322 * **closest/largest/mode O** - the orphans in tabular format 234 * **closest/largest/mode O** - the orphans in tabular format
323 * **closest/largest/mode P** - the preview plots graph in a specified format: pdf, png or svg 235 * **closest/largest/mode P** - the preview plots graph in pdf format
324 * **closest/largest/mode S** - the matched pairs in gff format 236 * **closest/largest/mode S** - the matched pairs in gff format
325 237
238 -----
326 239
327 **Options** 240 **Options**
328 241
329 * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types. 242 * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.
330 * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method). 243 * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method).
331 * **Distance upstream from a peak to allow a pair** - Distance upstream from a Watson peak to allow a Crick pair. 244 * **Distance upstream from a peak to allow a pair** - Distance upstream from a Watson peak to allow a Crick pair.
332 * **Distance downstream from a peak to allow a pair** - Distance downstream from a Watson peak to allow a Crick pair. 245 * **Distance downstream from a peak to allow a pair** - Distance downstream from a Watson peak to allow a Crick pair.
333 * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold. 246 * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold.
334 * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold. 247 * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold.
335 * **Output format for graph** - Output format for graph.
336 * **Sort output by chromosomes in** - Output will be sorted by chromsome in the specified order. 248 * **Sort output by chromosomes in** - Output will be sorted by chromsome in the specified order.
337 * **Sort output by score?** - If yes, output will be sorted by score in the specified order. 249 * **Sort output by score?** - If yes, output will be sorted by score in the specified order.
338 * **Summary output format** - Format for summary output. 250 * **Summary output format** - Format for summary output.
339 251
340 </help> 252 </help>