Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions
comparison chicSignificantInteractions.xml @ 8:640e0e45518a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author | iuc |
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date | Wed, 18 Oct 2023 10:52:55 +0000 |
parents | 6001400eed99 |
children |
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7:6ef732512682 | 8:640e0e45518a |
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5 <import>macros.xml</import> | 5 <import>macros.xml</import> |
6 </macros> | 6 </macros> |
7 <expand macro="requirements" /> | 7 <expand macro="requirements" /> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 #import re | 9 #import re |
10 | 10 |
11 mkdir interactionFiles && | 11 @BINARY@ |
12 mkdir targetFolder && | |
13 mkdir significantFilesFolder && | |
14 | |
15 #if $tar_input_conditional.tar_input_selector == 'tar_input': | |
16 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && | |
17 tar -C interactionFiles -xvf viewpoints.tar && | |
18 #else: | |
19 #for $file in $tar_input_conditional.interactionFiles: | |
20 #set identifier = @ESCAPE_IDENTIFIER_FILE@ | |
21 ln -s '$file' 'interactionFiles/$identifier' && | |
22 #end for | |
23 #end if | |
24 | 12 |
25 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': | 13 --interactionFile '$interactionFile' |
26 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) | 14 |
27 #end if | |
28 @BINARY@ | |
29 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': | |
30 --interactionFile $interactonfileslist | |
31 --computeSampleNumber $batchmode_conditional.computeSampleNumber | |
32 #else: | |
33 --interactionFile '$batchmode_conditional.interactionFilesOrderFile' | |
34 --interactionFileFolder interactionFiles | |
35 --batchMode | |
36 --targetFileList targetListFile.txt | |
37 --writeFileNamesToFile significantFiles.txt | |
38 --computeSampleNumber $batchmode_conditional.computeSampleNumber | |
39 #end if | |
40 | |
41 --pValue $pvalue | 15 --pValue $pvalue |
42 | 16 |
43 #if $filter_conditional.filter_selector == 'optionXfold': | 17 #if $filter_conditional.filter_selector == 'optionXfold': |
44 --xFoldBackground $filter_conditional.xfold | 18 --xFoldBackground $filter_conditional.xfold |
45 #else: | 19 #else: |
46 --loosePValue $filter_conditional.loosePvalue | 20 --loosePValue $filter_conditional.loosePvalue |
47 | 21 |
48 #end if | 22 #end if |
49 --backgroundModelFile '$backgroundModelFile' | 23 --backgroundModelFile '$backgroundModelFile' |
50 --resolution $resolution | |
51 --peakInteractionsThreshold $peakInteractionsThreshold | 24 --peakInteractionsThreshold $peakInteractionsThreshold |
52 --range $rangeUpstream $rangeDownstream | 25 --range $rangeUpstream $rangeDownstream |
53 --targetFolder targetFolder | 26 --combinationMode $mode_selector |
54 --outputFolder significantFilesFolder | 27 --outFileNameSignificant significant.hdf5 |
28 --outFileNameTarget target.hdf5 | |
55 $truncateZeroPvalues | 29 $truncateZeroPvalues |
56 --fixateRange $fixateRange | 30 --fixateRange $fixateRange |
57 -suffix significant_interactions.txt | |
58 --threads @THREADS@ | 31 --threads @THREADS@ |
59 | 32 |
60 #if $tar: | |
61 && cd targetFolder | |
62 && tar -cvf ../targetFolder.tar * | |
63 && cd .. | |
64 && rm -rf targetFolder | |
65 | |
66 && cd significantFilesFolder | |
67 && tar -cvf ../significantFilesFolder.tar * | |
68 && cd .. | |
69 && rm -rf significantFilesFolder | |
70 | |
71 #end if | |
72 ]]> </command> | 33 ]]> </command> |
73 <inputs> | 34 <inputs> |
74 <conditional name="tar_input_conditional"> | 35 <param name="interactionFile" type="data" format="h5" label="The interaction data file created by chicViewpoint" /> |
75 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> | 36 |
76 <option value="tar_input">Tar file</option> | 37 <param name="pvalue" type="float" value="0.05" label="P-value of interaction to be accepted as significant" /> |
77 <option value="interval_input" selected="True">Interval files</option> | |
78 </param> | |
79 <when value="tar_input"> | |
80 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" /> | |
81 </when> | |
82 <when value="interval_input"> | |
83 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" /> | |
84 </when> | |
85 </conditional> | |
86 <conditional name="batchmode_conditional"> | |
87 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> | |
88 <option value="optionBatchmode">Batch processing</option> | |
89 <option value="optionSinglemode" selected="True">Single file processing</option> | |
90 </param> | |
91 <when value="optionBatchmode"> | |
92 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" /> | |
93 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." /> | |
94 </when> | |
95 <when value="optionSinglemode"> | |
96 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." /> | |
97 </when> | |
98 </conditional> | |
99 <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant" /> | |
100 <conditional name="filter_conditional"> | 38 <conditional name="filter_conditional"> |
101 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions"> | 39 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions"> |
102 <option value="optionXfold">x-fold over mean background</option> | 40 <option value="optionXfold">x-fold over mean background</option> |
103 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option> | 41 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option> |
104 </param> | 42 </param> |
105 <when value="optionXfold"> | 43 <when value="optionXfold"> |
106 <param name='xfold' type="float" value='2.0' label="X-fold over mean background to be accepted." help='Filter x-fold over background. Used to merge neighboring bins with a broader peak but | 44 <param name="xfold" type="float" value="2.0" label="X-fold over mean background to be accepted." help="Filter x-fold over background. |
107 less significant interactions to one peak with high significance. Used only for pValue option.' /> | 45 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. Used only for pValue option." /> |
108 </when> | 46 </when> |
109 <when value="optionLoosePvalue"> | 47 <when value="optionLoosePvalue"> |
110 <param name='loosePvalue' type="float" value='0.3' label="Loose p-value" help='loose p-value threshold value to filter target regions in a first round. | 48 <param name="loosePvalue" type="float" value="0.3" label="Loose p-value" help="loose p-value threshold value to filter target regions in a first round. |
111 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. | 49 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. |
112 Used only for pValue option.' /> | 50 Used only for pValue option." /> |
113 </when> | 51 </when> |
114 </conditional> | 52 </conditional> |
115 <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" /> | 53 |
116 <param argument="--peakInteractionsThreshold" type="integer" value="5" label="Minimum interactions" help='The minimum number of interactions a detected peaks needs to have to be considered.' /> | 54 <param argument="--backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" /> |
117 <param argument="--resolution" type="integer" value="1000" label="Bin resolution of the used data" help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution. | 55 <param argument="--peakInteractionsThreshold" type="integer" value="5" label="Minimum interactions" help="The minimum number of interactions a detected peaks needs to have to be considered." /> |
118 This value is used to merge neighboring bins.' /> | 56 |
119 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> | 57 <param name="mode_selector" type="select" label="Process matrices independently or combine always two (for differential analysis preparation)"> |
120 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> | 58 <option value="dual">Dual</option> |
121 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.' /> | 59 <option value="single" selected="True">Single</option> |
122 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision." /> | 60 </param> |
123 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large." /> | 61 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." /> |
62 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help="Defines the region upstream of a reference point which should be considered in the analysis." /> | |
63 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help="Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin." /> | |
64 <param name="truncateZeroPvalues" type="boolean" truevalue="--truncateZeroPvalues" falsevalue="" checked="false" label="Truncate zeros by setting them to one." help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision." /> | |
124 </inputs> | 65 </inputs> |
66 | |
125 <outputs> | 67 <outputs> |
126 <collection name="significantFilesCollection" type="list" label="Significant files"> | 68 <data name="significantFile" from_work_dir="significant.hdf5" format="h5" label="${tool.name} significant file" /> |
127 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" /> | 69 <data name="targetFile" from_work_dir="target.hdf5" format="h5" label="${tool.name} target file" /> |
128 </collection> | |
129 <collection name="targetFilesCollection" type="list" label="Target files"> | |
130 <discover_datasets pattern="__name__" format="interval" directory="targetFolder" /> | |
131 </collection> | |
132 <data name="significantFileNames" from_work_dir="significantFiles.txt" format="txt" label="${tool.name} significant file names"> | |
133 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> | |
134 </data> | |
135 <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names"> | |
136 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> | |
137 </data> | |
138 <data name="targetFolderTar" from_work_dir="targetFolder.tar" format="tar" label="Target files tar"> | |
139 <filter>tar</filter> | |
140 </data> | |
141 <data name="significantFilesFolderTar" from_work_dir="significantFilesFolder.tar" format="tar" label="Significant files tar"> | |
142 <filter>tar</filter> | |
143 </data> | |
144 </outputs> | 70 </outputs> |
145 <tests> | 71 <tests> |
146 <test> | 72 <test> |
147 <conditional name="tar_input_conditional"> | 73 <param name="interactionFile" value="cHi-C/chicViewpoint/two_matrices.hdf5" /> |
148 <param name="tar_input_selector" value='interval_input' /> | 74 <param name="pvalue" value="0.2" /> |
149 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" /> | |
150 </conditional> | |
151 <conditional name="batchmode_conditional"> | |
152 <param name="batchmode_selector" value='optionBatchmode' /> | |
153 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> | |
154 <param name="computeSampleNumber" value='2' /> | |
155 </conditional> | |
156 <param name="pvalue" value='0.2' /> | |
157 | 75 |
158 <conditional name="filter_conditional"> | 76 <conditional name="filter_conditional"> |
159 <param name="filter_selector" value='optionLoosePvalue' /> | 77 <param name="filter_selector" value="optionLoosePvalue" /> |
160 <param name="loosePvalue" value='0.5' /> | 78 <param name="loosePvalue" value="0.5" /> |
161 </conditional> | 79 </conditional> |
162 | 80 <param name="mode_selector" value="dual" /> |
163 <param name="backgroundModelFile" value="cHi-C/background.txt" /> | 81 <param name="backgroundModelFile" value="cHi-C/background.txt" /> |
164 <param name="rangeUpstream" value="200000" /> | 82 <param name="rangeUpstream" value="200000" /> |
165 <param name="rangeDownstream" value="200000" /> | 83 <param name="rangeDownstream" value="200000" /> |
166 | 84 |
167 <output_collection name="significantFilesCollection" type="list" count="6"> | 85 <output name="significantFile" ftype="h5"> |
168 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval"> | 86 <assert_contents> |
169 <assert_contents> | 87 <has_h5_attribute key="combinationMode" value="dual" /> |
170 <has_text text="4480000" /> | 88 <has_h5_attribute key="mode_preselection" value="loosePValue" /> |
171 <has_text text="chr1" /> | 89 <has_h5_attribute key="type" value="significant" /> |
172 <has_text text="Sox17" /> | 90 </assert_contents> |
173 <has_text text="810.0" /> | 91 </output> |
174 <has_text text="interactions" /> | 92 |
175 </assert_contents> | 93 <output name="targetFile" ftype="h5"> |
176 </element> | 94 <assert_contents> |
177 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval"> | 95 <has_h5_attribute key="combinationMode" value="dual" /> |
178 <assert_contents> | 96 <has_h5_attribute key="mode_preselection" value="loosePValue" /> |
179 <has_text text="14274000" /> | 97 <has_h5_attribute key="type" value="target" /> |
180 <has_text text="chr1" /> | 98 </assert_contents> |
181 <has_text text="Eya1" /> | 99 </output> |
182 <has_text text="interactions" /> | |
183 </assert_contents> | |
184 </element> | |
185 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4" /> | |
186 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval"> | |
187 <assert_contents> | |
188 <has_text text="4480000" /> | |
189 <has_text text="chr1" /> | |
190 <has_text text="Sox17" /> | |
191 <has_text text="interactions" /> | |
192 <has_text text="93000" /> | |
193 <has_text text="978.0" /> | |
194 </assert_contents> | |
195 </element> | |
196 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4" /> | |
197 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval"> | |
198 <assert_contents> | |
199 <has_text text="19077000" /> | |
200 <has_text text="chr1" /> | |
201 <has_text text="Tfap2d" /> | |
202 <has_text text="interactions" /> | |
203 <has_text text="-15000" /> | |
204 </assert_contents> | |
205 </element> | |
206 </output_collection> | |
207 <output_collection name="targetFilesCollection" type="list" count="3"> | |
208 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval"> | |
209 <assert_contents> | |
210 <has_text text="4555000" /> | |
211 <has_text text="chr1" /> | |
212 <has_text text="p-value" /> | |
213 <has_text text="interactions" /> | |
214 </assert_contents> | |
215 </element> | |
216 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" /> | |
217 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" ftype="interval"> | |
218 <assert_contents> | |
219 <has_text text="19143000" /> | |
220 <has_text text="chr1" /> | |
221 <has_text text="p-value" /> | |
222 <has_text text="19150000" /> | |
223 </assert_contents> | |
224 </element> | |
225 </output_collection> | |
226 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" /> | |
227 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" /> | |
228 </test> | 100 </test> |
229 <test> | 101 |
230 <conditional name="tar_input_conditional"> | |
231 <param name="tar_input_selector" value='interval_input' /> | |
232 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" /> | |
233 </conditional> | |
234 <conditional name="batchmode_conditional"> | |
235 <param name="batchmode_selector" value='optionSinglemode' /> | |
236 <param name="computeSampleNumber" value="1" /> | |
237 </conditional> | |
238 <param name="pvalue" value='0.2' /> | |
239 | |
240 <conditional name="filter_conditional"> | |
241 <param name="filter_selector" value='optionXfold' /> | |
242 <param name="xfold" value='1.5' /> | |
243 </conditional> | |
244 | |
245 <param name="backgroundModelFile" value="cHi-C/background.txt" /> | |
246 <param name="rangeUpstream" value="200000" /> | |
247 <param name="rangeDownstream" value="200000" /> | |
248 | |
249 <output_collection name="significantFilesCollection" type="list" count="2"> | |
250 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.txt" ftype="interval" lines_diff="4" /> | |
251 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval"> | |
252 <assert_contents> | |
253 <has_text text="14295000" /> | |
254 <has_text text="chr1" /> | |
255 <has_text text="Eya1" /> | |
256 <has_text text="interactions" /> | |
257 </assert_contents> | |
258 </element> | |
259 </output_collection> | |
260 <output_collection name="targetFilesCollection" type="list" count="2"> | |
261 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" /> | |
262 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4" /> | |
263 </output_collection> | |
264 </test> | |
265 | |
266 <test> | |
267 <conditional name="tar_input_conditional"> | |
268 <param name="tar_input_selector" value='interval_input' /> | |
269 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" /> | |
270 </conditional> | |
271 <conditional name="batchmode_conditional"> | |
272 <param name="batchmode_selector" value='optionBatchmode' /> | |
273 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> | |
274 <param name="computeSampleNumber" value='2' /> | |
275 </conditional> | |
276 <param name="pvalue" value='0.2' /> | |
277 | |
278 <conditional name="filter_conditional"> | |
279 <param name="filter_selector" value='optionLoosePvalue' /> | |
280 <param name="loosePvalue" value='0.5' /> | |
281 </conditional> | |
282 | |
283 <param name="backgroundModelFile" value="cHi-C/background.txt" /> | |
284 <param name="rangeUpstream" value="200000" /> | |
285 <param name="rangeDownstream" value="200000" /> | |
286 | |
287 <param name='tar' value='True' /> | |
288 | |
289 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> | |
290 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> | |
291 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" /> | |
292 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" /> | |
293 </test> | |
294 | |
295 <test> | |
296 <conditional name="tar_input_conditional"> | |
297 <param name="tar_input_selector" value='tar_input' /> | |
298 <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar" /> | |
299 </conditional> | |
300 <conditional name="batchmode_conditional"> | |
301 <param name="batchmode_selector" value='optionBatchmode' /> | |
302 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' /> | |
303 <param name="computeSampleNumber" value='2' /> | |
304 </conditional> | |
305 <param name="pvalue" value='0.2' /> | |
306 | |
307 <conditional name="filter_conditional"> | |
308 <param name="filter_selector" value='optionLoosePvalue' /> | |
309 <param name="loosePvalue" value='0.5' /> | |
310 </conditional> | |
311 | |
312 <param name="backgroundModelFile" value="cHi-C/background.txt" /> | |
313 <param name="rangeUpstream" value="200000" /> | |
314 <param name="rangeDownstream" value="200000" /> | |
315 | |
316 <param name='tar' value='True' /> | |
317 | |
318 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> | |
319 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> | |
320 | |
321 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000' /> | |
322 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000' /> | |
323 </test> | |
324 </tests> | 102 </tests> |
325 <help><![CDATA[ | 103 <help><![CDATA[ |
326 | 104 |
327 Significant interaction detection | 105 Significant interaction detection |
328 ================================= | 106 ================================= |