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author greg
date Wed, 02 Dec 2015 16:14:07 -0500
parents d455f14530dc
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9:6469dda597d6 10:b52d6705aed0
9 <![CDATA[ 9 <![CDATA[
10 python $__tool_directory__/cwpair2.py 10 python $__tool_directory__/cwpair2.py
11 #for $i in $input: 11 #for $i in $input:
12 --input "${i}" "${i.hid}" 12 --input "${i}" "${i.hid}"
13 #end for 13 #end for
14 --method $method
15 --up_distance $up_distance 14 --up_distance $up_distance
16 --down_distance $down_distance 15 --down_distance $down_distance
16 --method $method
17 --binsize $binsize 17 --binsize $binsize
18 --threshold_format $threshold_format_cond.threshold_format 18 --threshold_format $threshold_format_cond.threshold_format
19 #if str($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 24 --output_files $output_files
25 --sort_score $sort_score
26 --statistics_output "$statistics_output" 25 --statistics_output "$statistics_output"
27 ]]> 26 ]]>
28 </command> 27 </command>
29 <inputs> 28 <inputs>
30 <param name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" /> 29 <param name="input" type="data" format="gff" multiple="True" label="Find matched pairs on" />
30 <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" />
31 <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" />
31 <param name="method" type="select" label="Method of finding a match"> 32 <param name="method" type="select" label="Method of finding a match">
32 <option value="mode" selected="True">Mode</option> 33 <option value="mode" selected="True">Mode</option>
33 <option value="closest">Closest</option> 34 <option value="closest">Closest</option>
34 <option value="largest">Largest</option> 35 <option value="largest">Largest</option>
35 <option value="all">All</option> 36 <option value="all">All</option>
36 </param> 37 </param>
37 <param name="up_distance" type="integer" value="50" min="0" label="Distance upstream from a peak to allow a pair" />
38 <param name="down_distance" type="integer" value="100" min="0" label="Distance downstream from a peak to allow a pair" />
39 <param name="binsize" type="integer" value="1" min="0" label="Width of bins for frequency plots and mode calculation" help="Value 1 implies no bins" /> 38 <param name="binsize" type="integer" value="1" min="0" label="Width of bins for frequency plots and mode calculation" help="Value 1 implies no bins" />
40 <conditional name="threshold_format_cond"> 39 <conditional name="threshold_format_cond">
41 <param name="threshold_format" type="select" label="Filter using"> 40 <param name="threshold_format" type="select" label="Filter using">
42 <option value="relative_threshold" selected="True">Relative threshold</option> 41 <option value="relative_threshold" selected="True">Relative threshold</option>
43 <option value="absolute_threshold">Absolute threshold</option> 42 <option value="absolute_threshold">Absolute threshold</option>
48 <when value="absolute_threshold"> 47 <when value="absolute_threshold">
49 <param name="absolute_threshold" type="float" value="0.0" min="0.0" label="Absolute value to filter below" /> 48 <param name="absolute_threshold" type="float" value="0.0" min="0.0" label="Absolute value to filter below" />
50 </when> 49 </when>
51 </conditional> 50 </conditional>
52 <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." > 51 <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." >
53 <option value="simple" selected="True">matched pairs only (S)</option> 52 <option value="all" selected="True">no restrictions (output everything: C,D,F,O,P,MP)</option>
54 <option value="simple_orphan">matched pairs and orphans only (O,S)</option> 53 <option value="matched_pair">matched pairs only (MP)</option>
55 <option value="simple_orphan_detail">matched pairs, orphans and details only (D,O,S)</option> 54 <option value="matched_pair_orphan">matched pairs and orphans only (O,MP)</option>
56 <option value="all">no restrictions (output everything: C,D,F,O,P,S)</option> 55 <option value="matched_pair_orphan_detail">matched pairs, orphans and details only (D,O,MP)</option>
57 </param>
58 <param name="sort_score" type="select" label="Sort output by score?">
59 <option value="no" selected="True">No</option>
60 <option value="asc">Yes, in ascending order</option>
61 <option value="desc">Yes, in descending order</option>
62 </param> 56 </param>
63 </inputs> 57 </inputs>
64 <outputs> 58 <outputs>
65 <collection name="closest_C_pdf" type="list" label="closest C: ${tool.name} on ${on_string}"> 59 <data name="statistics_output" format="tabular" label="Statistics Table: ${tool.name} on ${on_string}" />
66 <filter>output_files == "all" and method in ["all", "closest"]</filter> 60 <collection name="H" type="list" label="Statistics Histogram: ${tool.name} on ${on_string}">
67 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_C" ext="pdf" visible="false" /> 61 <filter>output_files == "all"</filter>
62 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="H" ext="pdf" visible="false" />
68 </collection> 63 </collection>
69 <collection name="largest_C_pdf" type="list" label="largest C: ${tool.name} on ${on_string}"> 64 <collection name="D" type="list" label="Data D: ${tool.name} on ${on_string}">
70 <filter>output_files == "all" and method in ["all", "largest"]</filter> 65 <filter>output_files in ["all", "matched_pair_orphan_detail"]</filter>
71 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_C" ext="pdf" visible="false" /> 66 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="data_D" ext="tabular" visible="false" />
72 </collection> 67 </collection>
73 <collection name="mode_C_pdf" type="list" label="mode C: ${tool.name} on ${on_string}"> 68 <collection name="O" type="list" label="Data O: ${tool.name} on ${on_string}">
74 <filter>output_files == "all" and method in ["all", "mode"]</filter> 69 <filter>output_files in ["all", "matched_pair_orphan", "matched_pair_orphan_detail"]</filter>
75 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_C" ext="pdf" visible="false" /> 70 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="data_O" ext="tabular" visible="false" />
76 </collection> 71 </collection>
77 <collection name="closest_D" type="list" label="closest D: ${tool.name} on ${on_string}"> 72 <collection name="MP" type="list" label="Data MP: ${tool.name} on ${on_string}">
78 <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "closest"]</filter> 73 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="data_MP" ext="gff" visible="false" />
79 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_D" ext="tabular" visible="false" />
80 </collection> 74 </collection>
81 <collection name="largest_D" type="list" label="largest D: ${tool.name} on ${on_string}">
82 <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "largest"]</filter>
83 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_D" ext="tabular" visible="false" />
84 </collection>
85 <collection name="mode_D" type="list" label="mode D: ${tool.name} on ${on_string}">
86 <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "mode"]</filter>
87 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_D" ext="tabular" visible="false" />
88 </collection>
89 <collection name="closest_F_pdf" type="list" label="closest F: ${tool.name} on ${on_string}">
90 <filter>output_files == "all" and method in ["all", "closest"]</filter>
91 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_F" ext="pdf" visible="false" />
92 </collection>
93 <collection name="largest_F_pdf" type="list" label="largest F: ${tool.name} on ${on_string}">
94 <filter>output_files == "all" and method in ["all", "largest"]</filter>
95 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_F" ext="pdf" visible="false" />
96 </collection>
97 <collection name="mode_F_pdf" type="list" label="mode F: ${tool.name} on ${on_string}">
98 <filter>output_files == "all" and method in ["all", "mode"]</filter>
99 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_F" ext="pdf" visible="false" />
100 </collection>
101 <collection name="closest_O" type="list" label="closest O: ${tool.name} on ${on_string}">
102 <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "closest"]</filter>
103 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_O" ext="tabular" visible="false" />
104 </collection>
105 <collection name="largest_O" type="list" label="largest O: ${tool.name} on ${on_string}">
106 <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "largest"]</filter>
107 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_O" ext="tabular" visible="false" />
108 </collection>
109 <collection name="mode_O" type="list" label="mode O: ${tool.name} on ${on_string}">
110 <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "mode"]</filter>
111 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_O" ext="tabular" visible="false" />
112 </collection>
113 <collection name="closest_P_pdf" type="list" label="closest P: ${tool.name} on ${on_string}">
114 <filter>output_files == "all" and method in ["all", "closest"]</filter>
115 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_P" ext="pdf" visible="false" />
116 </collection>
117 <collection name="largest_P_pdf" type="list" label="largest P: ${tool.name} on ${on_string}">
118 <filter>output_files == "all" and method in ["all", "largest"]</filter>
119 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_P" ext="pdf" visible="false" />
120 </collection>
121 <collection name="mode_P_pdf" type="list" label="mode P: ${tool.name} on ${on_string}">
122 <filter>output_files == "all" and method in ["all", "mode"]</filter>
123 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_P" ext="pdf" visible="false" />
124 </collection>
125 <collection name="closest_S" type="list" label="closest S: ${tool.name} on ${on_string}">
126 <filter>method in ["all", "closest"]</filter>
127 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="closest_S" ext="gff" visible="false" />
128 </collection>
129 <collection name="largest_S" type="list" label="largest S: ${tool.name} on ${on_string}">
130 <filter>method in ["all", "largest"]</filter>
131 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="largest_S" ext="gff" visible="false" />
132 </collection>
133 <collection name="mode_S" type="list" label="mode S: ${tool.name} on ${on_string}">
134 <filter>method in ["all", "mode"]</filter>
135 <discover_datasets pattern="(?P&lt;designation&gt;.*)" directory="mode_S" ext="gff" visible="false" />
136 </collection>
137 <data name="statistics_output" format="tabular" label="Statistics: ${tool.name} on ${on_string}" />
138 </outputs> 75 </outputs>
139 <tests> 76 <tests>
140 <test> 77 <test>
141 <param name="input" value="cwpair2_input1.gff" /> 78 <param name="input" value="cwpair2_input1.gff" />
142 <param name="method" value="all" />
143 <param name="up_distance" value="25" /> 79 <param name="up_distance" value="25" />
144 <param name="down_distance" value="100" /> 80 <param name="down_distance" value="100" />
81 <param name="method" value="all" />
145 <param name="binsize" value="1" /> 82 <param name="binsize" value="1" />
146 <param name="threshold_format" value="relative_threshold" /> 83 <param name="threshold_format" value="relative_threshold" />
147 <param name="relative_threshold" value="0.0" /> 84 <param name="relative_threshold" value="0.0" />
148 <param name="output_files" value="simple" /> 85 <param name="output_files" value="matched_pair" />
149 <param name="sort_score" value="asc" /> 86 <output name="statistics_output" file="statistics1.tabular" ftype="tabular" />
150 <output_collection name="closest_S" type="list"> 87 <output_collection name="MP" type="list">
151 <element name="closest_S_data_1_f0u25d100b1" file="closest_s_output1.gff" ftype="gff" /> 88 <element name="f0u25d100_on_data_1" file="closest_mp_output1.gff" ftype="gff" />
89 <element name="f0u25d100_on_data_1" file="largest_mp_output1.gff" ftype="gff" />
90 <element name="f0u25d100_on_data_1" file="mode_mp_output1.gff" ftype="gff" />
152 </output_collection> 91 </output_collection>
153 <output_collection name="largest_S" type="list">
154 <element name="largest_S_data_1_f0u25d100b1" file="largest_s_output1.gff" ftype="gff" />
155 </output_collection>
156 <output_collection name="mode_S" type="list">
157 <element name="mode_S_data_1_f0u25d100b1" file="mode_s_output1.gff" ftype="gff" />
158 </output_collection>
159 <output name="statistics_output" file="statistics1.tabular" ftype="tabular" />
160 </test> 92 </test>
161 <test> 93 <test>
162 <param name="input" value="cwpair2_input1.gff" /> 94 <param name="input" value="cwpair2_input1.gff" />
163 <param name="method" value="all" />
164 <param name="up_distance" value="50" /> 95 <param name="up_distance" value="50" />
165 <param name="down_distance" value="100" /> 96 <param name="down_distance" value="100" />
97 <param name="method" value="all" />
166 <param name="binsize" value="1" /> 98 <param name="binsize" value="1" />
167 <param name="threshold_format" value="relative_threshold" /> 99 <param name="threshold_format" value="relative_threshold" />
168 <param name="relative_threshold" value="0.0" /> 100 <param name="relative_threshold" value="0.0" />
169 <param name="output_files" value="all" /> 101 <param name="output_files" value="all" />
170 <param name="sort_score" value="no" /> 102 <output name="statistics_output" file="statistics2.tabular" ftype="tabular" />
171 <output_collection name="closest_D" type="list"> 103 <output_collection name="H" type="list">
172 <element name="closest_D_data_1_f0u50d100b1" file="closest_d_output2.tabular" ftype="tabular" /> 104 <element name="histogram_C_mode_f0u50d100_on_data_1" file="mode_c_output2.pdf" ftype="pdf" compare="sim_size" />
105 <element name="histogram_F_closest_f0u50d100_on_data_1" file="closest_f_output2.pdf" ftype="pdf" compare="sim_size" />
106 <element name="histogram_F_largest_f0u50d100_on_data_1" file="largest_f_output2.pdf" ftype="pdf" compare="sim_size" />
107 <element name="histogram_F_mode_f0u50d100_on_data_1" file="mode_f_output2.pdf" ftype="pdf" compare="sim_size" />
108 <element name="histogram_P_mode_f0u50d100_on_data_1" file="mode_p_output2.pdf" ftype="pdf" compare="sim_size" />
173 </output_collection> 109 </output_collection>
174 <output_collection name="closest_F" type="list"> 110 <output_collection name="D" type="list">
175 <element name="closest_F_data_1_f0u50d100b1" file="closest_f_output2.pdf" ftype="pdf" compare="sim_size" /> 111 <element name="data_D_closest_f0u50d100_on_data_1" file="closest_d_output2.tabular" ftype="tabular" />
112 <element name="data_D_largest_f0u50d100_on_data_1" file="largest_d_output2.tabular" ftype="tabular" />
113 <element name="data_D_mode_f0u50d100_on_data_1" file="mode_d_output2.tabular" ftype="tabular" />
176 </output_collection> 114 </output_collection>
177 <output_collection name="closest_O" type="list"> 115 <output_collection name="O" type="list">
178 <element name="closest_O_data_1_f0u50d100b1" file="closest_o_output2.tabular" ftype="tabular" /> 116 <element name="data_O_closest_f0u50d100_on_data_1" file="closest_o_output2.tabular" ftype="tabular" />
117 <element name="data_O_largest_f0u50d100_on_data_1" file="largest_o_output2.tabular" ftype="tabular" />
118 <element name="data_O_mode_f0u50d100_on_data_1" file="mode_o_output2.tabular" ftype="tabular" />
179 </output_collection> 119 </output_collection>
180 <output_collection name="closest_S" type="list"> 120 <output_collection name="MP" type="list">
181 <element name="closest_S_data_1_f0u50d100b1" file="closest_s_output2.gff" ftype="gff" /> 121 <element name="data_MP_closest_f0u50d100_on_data_1" file="closest_mp_output2.gff" ftype="gff" />
122 <element name="data_MP_largest_f0u50d100_on_data_1" file="largest_mp_output2.gff" ftype="gff" />
123 <element name="data_MP_mode_f0u50d100_on_data_1" file="mode_mp_output2.gff" ftype="gff" />
182 </output_collection> 124 </output_collection>
183 <output_collection name="largest_D" type="list">
184 <element name="largest_D_data_1_f0u50d100b1" file="largest_d_output2.tabular" ftype="tabular" />
185 </output_collection>
186 <output_collection name="largest_F" type="list">
187 <element name="largest_F_data_1_f0u50d100b1" file="largest_f_output2.pdf" ftype="pdf" compare="sim_size" />
188 </output_collection>
189 <output_collection name="largest_O" type="list">
190 <element name="largest_O_data_1_f0u50d100b1" file="largest_o_output2.tabular" ftype="tabular" />
191 </output_collection>
192 <output_collection name="largest_S" type="list">
193 <element name="largest_S_data_1_f0u50d100b1" file="largest_s_output2.gff" ftype="gff" />
194 </output_collection>
195 <output_collection name="mode_C" type="list">
196 <element name="mode_C_data_1_f0u50d100b1" file="mode_c_output2.pdf" ftype="pdf" compare="sim_size" />
197 </output_collection>
198 <output_collection name="mode_D" type="list">
199 <element name="mode_D_data_1_f0u50d100b1" file="mode_d_output2.tabular" ftype="tabular" />
200 </output_collection>
201 <output_collection name="mode_F" type="list">
202 <element name="mode_F_data_1_f0u50d100b1" file="mode_f_output2.pdf" ftype="pdf" compare="sim_size" />
203 </output_collection>
204 <output_collection name="mode_O" type="list">
205 <element name="mode_O_data_1_f0u50d100b1" file="mode_o_output2.tabular" ftype="tabular" />
206 </output_collection>
207 <output_collection name="mode_P" type="list">
208 <element name="mode_P_data_1_f0u50d100b1" file="mode_p_output2.pdf" ftype="pdf" compare="sim_size" />
209 </output_collection>
210 <output_collection name="mode_S" type="list">
211 <element name="mode_S_data_1_f0u50d100b1" file="mode_s_output2.gff" ftype="gff" />
212 </output_collection>
213 <output name="statistics_output" file="statistics2.tabular" ftype="tabular" />
214 </test> 125 </test>
215 </tests> 126 </tests>
216 <help> 127 <help>
217 **What it does** 128 **What it does**
218 129
219 Takes a list of called peaks on both strands and produces a list of matched pairs and a list of unmatched orphans 130 Takes a list of called peaks on both strands and produces lists of matched pairs and unmatched peaks using a
220 using a specified method for finding matched pairs. Methods for finding matched pairs are mode, closest, largest 131 specified method for finding matched pairs. Methods for finding matched pairs are mode, closest, largest or
221 or all (where the analysis is run for each method). A statistics dataset is generated and a collection of datasets 132 all (where the analysis is run for each method). A statistics dataset is generated and a collection of datasets
222 is produced for each method as follows. 133 is produced for each method as follows.
223 134
135 **Data Files**
136
137 * **closest/largest/mode MP** - the Matched Pairs in gff format
138 * **closest/largest/mode O** - the Orphans in tabular format
139 * **closest/largest/mode D** - the Details in tabular format
140
141 **Statistics Files**
142
224 * **closest/largest/mode C** - the stastics graph in pdf format 143 * **closest/largest/mode C** - the stastics graph in pdf format
225 * **closest/largest/mode D** - the details in tabular format 144 * **closest/largest/mode P** - the preview plots graph in pdf format
226 * **closest/largest/mode F** - the final plots graph in pdf format 145 * **closest/largest/mode F** - the final plots graph in pdf format
227 * **closest/largest/mode O** - the orphans in tabular format
228 * **closest/largest/mode P** - the preview plots graph in pdf format
229 * **closest/largest/mode S** - the matched pairs in gff format
230 146
231 ----- 147 -----
232 148
233 **Options** 149 **Options**
234 150
235 * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.
236 * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method). 151 * **Method of finding match** - Method of finding matched pair, mode, closest, largest, or all (run with each method).
237 * **Distance upstream from a peak to allow a pair** - Distance upstream from a Watson peak to allow a Crick pair. 152 * **Distance upstream from a peak to allow a pair** - Distance upstream from a Watson peak to allow a Crick pair.
238 * **Distance downstream from a peak to allow a pair** - Distance downstream from a Watson peak to allow a Crick pair. 153 * **Distance downstream from a peak to allow a pair** - Distance downstream from a Watson peak to allow a Crick pair.
239 * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold. 154 * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold.
240 * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold. 155 * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold.
241 * **Sort output by chromosomes in** - Output will be sorted by chromsome in the specified order. 156 * **Output files** - Restrict output dataset collections to matched pairs only or one of several combinations of collection types.
242 * **Sort output by score?** - If yes, output will be sorted by score in the specified order.
243 * **Summary output format** - Format for summary output.
244 157
245 </help> 158 </help>
246 <expand macro="citations" /> 159 <expand macro="citations" />
247 </tool> 160 </tool>