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comparison cwpair2.xml @ 7:d455f14530dc draft

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Uploaded
author greg
date Tue, 24 Nov 2015 08:15:57 -0500
parents 9ed566138ecb
children b52d6705aed0
comparison
equal deleted inserted replaced
6:001551406848 7:d455f14530dc
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_chromosome $sort_chromosome
26 --sort_score $sort_score 25 --sort_score $sort_score
27 --statistics_output "$statistics_output" 26 --statistics_output "$statistics_output"
28 ]]> 27 ]]>
29 </command> 28 </command>
30 <inputs> 29 <inputs>
54 <option value="simple" selected="True">matched pairs only (S)</option> 53 <option value="simple" selected="True">matched pairs only (S)</option>
55 <option value="simple_orphan">matched pairs and orphans only (O,S)</option> 54 <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> 55 <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> 56 <option value="all">no restrictions (output everything: C,D,F,O,P,S)</option>
58 </param> 57 </param>
59 <param name="sort_chromosome" type="select" label="Sort output by chromosomes in" help="Chromosome strings that are not numeric will not be sorted" >
60 <option value="asc" selected="True">ascending order</option>
61 <option value="desc">descending order</option>
62 </param>
63 <param name="sort_score" type="select" label="Sort output by score?"> 58 <param name="sort_score" type="select" label="Sort output by score?">
64 <option value="no" selected="True">No</option> 59 <option value="no" selected="True">No</option>
65 <option value="asc">Yes, in ascending order</option> 60 <option value="asc">Yes, in ascending order</option>
66 <option value="desc">Yes, in descending order</option> 61 <option value="desc">Yes, in descending order</option>
67 </param> 62 </param>
149 <param name="down_distance" value="100" /> 144 <param name="down_distance" value="100" />
150 <param name="binsize" value="1" /> 145 <param name="binsize" value="1" />
151 <param name="threshold_format" value="relative_threshold" /> 146 <param name="threshold_format" value="relative_threshold" />
152 <param name="relative_threshold" value="0.0" /> 147 <param name="relative_threshold" value="0.0" />
153 <param name="output_files" value="simple" /> 148 <param name="output_files" value="simple" />
154 <param name="sort_chromosome" value="asc" />
155 <param name="sort_score" value="asc" /> 149 <param name="sort_score" value="asc" />
156 <output_collection name="closest_S" type="list"> 150 <output_collection name="closest_S" type="list">
157 <element name="closest_S_data_1_f0u25d100b1" file="closest_s_output1.gff" ftype="gff" /> 151 <element name="closest_S_data_1_f0u25d100b1" file="closest_s_output1.gff" ftype="gff" />
158 </output_collection> 152 </output_collection>
159 <output_collection name="largest_S" type="list"> 153 <output_collection name="largest_S" type="list">
171 <param name="down_distance" value="100" /> 165 <param name="down_distance" value="100" />
172 <param name="binsize" value="1" /> 166 <param name="binsize" value="1" />
173 <param name="threshold_format" value="relative_threshold" /> 167 <param name="threshold_format" value="relative_threshold" />
174 <param name="relative_threshold" value="0.0" /> 168 <param name="relative_threshold" value="0.0" />
175 <param name="output_files" value="all" /> 169 <param name="output_files" value="all" />
176 <param name="sort_chromosome" value="asc" />
177 <param name="sort_score" value="no" /> 170 <param name="sort_score" value="no" />
178 <output_collection name="closest_D" type="list"> 171 <output_collection name="closest_D" type="list">
179 <element name="closest_D_data_1_f0u50d100b1" file="closest_d_output2.tabular" ftype="tabular" /> 172 <element name="closest_D_data_1_f0u50d100b1" file="closest_d_output2.tabular" ftype="tabular" />
180 </output_collection> 173 </output_collection>
181 <output_collection name="closest_F" type="list"> 174 <output_collection name="closest_F" type="list">