Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions

comparison chicSignificantInteractions.xml @ 6:6001400eed99 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 2a0943e78bdc8ebb13f181399206a9eea37ed78f"
author iuc
date Tue, 16 Mar 2021 15:33:42 +0000
parents 38fa8a72ece6
children 640e0e45518a
comparison
equal deleted inserted replaced
5:6bc82c6d6620 6:6001400eed99
1 <tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.1"> 1 <tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>computes viewpoints with the given reference points and a background model</description> 2 <description>computes viewpoints with the given reference points and a background model</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">chicSignificantInteractions</token> 4 <token name="@BINARY@">chicSignificantInteractions</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
15 #if $tar_input_conditional.tar_input_selector == 'tar_input': 15 #if $tar_input_conditional.tar_input_selector == 'tar_input':
16 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar && 16 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar &&
17 tar -C interactionFiles -xvf viewpoints.tar && 17 tar -C interactionFiles -xvf viewpoints.tar &&
18 #else: 18 #else:
19 #for $file in $tar_input_conditional.interactionFiles: 19 #for $file in $tar_input_conditional.interactionFiles:
20 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 20 #set identifier = @ESCAPE_IDENTIFIER_FILE@
21
22 ln -s '$file' 'interactionFiles/$identifier' && 21 ln -s '$file' 'interactionFiles/$identifier' &&
23 #end for 22 #end for
24 #end if 23 #end if
25 24
26 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 25 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
28 #end if 27 #end if
29 @BINARY@ 28 @BINARY@
30 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 29 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
31 --interactionFile $interactonfileslist 30 --interactionFile $interactonfileslist
32 --computeSampleNumber $batchmode_conditional.computeSampleNumber 31 --computeSampleNumber $batchmode_conditional.computeSampleNumber
33
34 #else: 32 #else:
35 --interactionFile $batchmode_conditional.interactionFilesOrderFile 33 --interactionFile '$batchmode_conditional.interactionFilesOrderFile'
36 --interactionFileFolder interactionFiles 34 --interactionFileFolder interactionFiles
37 --batchMode 35 --batchMode
38 --targetFileList targetListFile.txt 36 --targetFileList targetListFile.txt
39 --writeFileNamesToFile significantFiles.txt 37 --writeFileNamesToFile significantFiles.txt
40 --computeSampleNumber $batchmode_conditional.computeSampleNumber 38 --computeSampleNumber $batchmode_conditional.computeSampleNumber
69 && tar -cvf ../significantFilesFolder.tar * 67 && tar -cvf ../significantFilesFolder.tar *
70 && cd .. 68 && cd ..
71 && rm -rf significantFilesFolder 69 && rm -rf significantFilesFolder
72 70
73 #end if 71 #end if
74 ]]></command> 72 ]]> </command>
75 <inputs> 73 <inputs>
76 <conditional name="tar_input_conditional"> 74 <conditional name="tar_input_conditional">
77 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> 75 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
78 <option value="tar_input">Tar file</option> 76 <option value="tar_input">Tar file</option>
79 <option value="interval_input" selected="True">Interval files</option> 77 <option value="interval_input" selected="True">Interval files</option>
80 </param> 78 </param>
81 <when value="tar_input"> 79 <when value="tar_input">
82 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/> 80 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" />
83 </when> 81 </when>
84 <when value="interval_input"> 82 <when value="interval_input">
85 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 83 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" />
86 </when> 84 </when>
87 </conditional> 85 </conditional>
88
89
90
91 <conditional name="batchmode_conditional"> 86 <conditional name="batchmode_conditional">
92 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> 87 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
93 <option value="optionBatchmode">Batch processing</option> 88 <option value="optionBatchmode">Batch processing</option>
94 <option value="optionSinglemode" selected="True">Single file processing</option> 89 <option value="optionSinglemode" selected="True">Single file processing</option>
95 </param> 90 </param>
96 <when value="optionBatchmode"> 91 <when value="optionBatchmode">
97 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> 92 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" />
98 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/> 93 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." />
99 </when> 94 </when>
100 <when value="optionSinglemode"> 95 <when value="optionSinglemode">
101 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/> 96 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files." />
102 </when> 97 </when>
103 </conditional> 98 </conditional>
104 <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant"/> 99 <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant" />
105 <conditional name="filter_conditional"> 100 <conditional name="filter_conditional">
106 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions"> 101 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions">
107 <option value="optionXfold">x-fold over mean background</option> 102 <option value="optionXfold">x-fold over mean background</option>
108 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option> 103 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option>
109 </param> 104 </param>
110 <when value="optionXfold"> 105 <when value="optionXfold">
111 <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 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
112 less significant interactions to one peak with high significance. Used only for pValue option.'/> 107 less significant interactions to one peak with high significance. Used only for pValue option.' />
113 </when> 108 </when>
114 <when value="optionLoosePvalue"> 109 <when value="optionLoosePvalue">
115 <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. 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.
116 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. 111 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance.
117 Used only for pValue option.'/> 112 Used only for pValue option.' />
118 </when> 113 </when>
119 </conditional> 114 </conditional>
120 <param argument="--backgroundModelFile" type="data" format='tabular' 115 <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
121 label="Background model" 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.' />
122 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.
123 <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.' />
124 <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. 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.' />
125 This value is used to merge neighboring bins.'/> 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.' />
126 <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.' /> 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.' />
127 <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.' /> 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." />
128 <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.'/> 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." />
129 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one."
130 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."/>
131 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
132 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
133 </inputs> 124 </inputs>
134 <outputs> 125 <outputs>
135 <collection name="significantFilesCollection" type="list" label="Significant files"> 126 <collection name="significantFilesCollection" type="list" label="Significant files">
136 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" /> 127 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" />
137 </collection> 128 </collection>
152 </data> 143 </data>
153 </outputs> 144 </outputs>
154 <tests> 145 <tests>
155 <test> 146 <test>
156 <conditional name="tar_input_conditional"> 147 <conditional name="tar_input_conditional">
157 <param name="tar_input_selector" value='interval_input'/> 148 <param name="tar_input_selector" value='interval_input' />
158 <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"/> 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" />
159 </conditional> 150 </conditional>
160 <conditional name="batchmode_conditional"> 151 <conditional name="batchmode_conditional">
161 <param name="batchmode_selector" value='optionBatchmode'/> 152 <param name="batchmode_selector" value='optionBatchmode' />
162 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 153 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
163 <param name="computeSampleNumber" value='2'/> 154 <param name="computeSampleNumber" value='2' />
164 </conditional> 155 </conditional>
165 <param name="pvalue" value='0.2'/> 156 <param name="pvalue" value='0.2' />
166 157
167 <conditional name="filter_conditional"> 158 <conditional name="filter_conditional">
168 <param name="filter_selector" value='optionLoosePvalue'/> 159 <param name="filter_selector" value='optionLoosePvalue' />
169 <param name="loosePvalue" value='0.5'/> 160 <param name="loosePvalue" value='0.5' />
170 </conditional> 161 </conditional>
171 162
172 <param name="backgroundModelFile" value="cHi-C/background.txt"/> 163 <param name="backgroundModelFile" value="cHi-C/background.txt" />
173 <param name="rangeUpstream" value="200000"/> 164 <param name="rangeUpstream" value="200000" />
174 <param name="rangeDownstream" value="200000"/> 165 <param name="rangeDownstream" value="200000" />
175 166
176 <output_collection name="significantFilesCollection" type="list" count="6"> 167 <output_collection name="significantFilesCollection" type="list" count="6">
177 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/> 168 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval">
178 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval" lines_diff="4"/> 169 <assert_contents>
179 <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"/> 170 <has_text text="4480000" />
180 171 <has_text text="chr1" />
181 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.txt" ftype="interval" lines_diff="4"/> 172 <has_text text="Sox17" />
182 <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"/> 173 <has_text text="810.0" />
183 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.txt" ftype="interval" lines_diff="4"/> 174 <has_text text="interactions" />
175 </assert_contents>
176 </element>
177 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" ftype="interval">
178 <assert_contents>
179 <has_text text="14274000" />
180 <has_text text="chr1" />
181 <has_text text="Eya1" />
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>
184 </output_collection> 206 </output_collection>
185
186 <output_collection name="targetFilesCollection" type="list" count="3"> 207 <output_collection name="targetFilesCollection" type="list" count="3">
187 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval" lines_diff="4"/> 208 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt" ftype="interval">
188 <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"/> 209 <assert_contents>
189 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt" ftype="interval" lines_diff="4"/> 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>
190 </output_collection> 225 </output_collection>
191 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/> 226 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" />
192 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/> 227 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" />
193 </test> 228 </test>
194 <test> 229 <test>
195 <conditional name="tar_input_conditional"> 230 <conditional name="tar_input_conditional">
196 <param name="tar_input_selector" value='interval_input'/> 231 <param name="tar_input_selector" value='interval_input' />
197 <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"/> 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" />
198 </conditional> 233 </conditional>
199 <conditional name="batchmode_conditional"> 234 <conditional name="batchmode_conditional">
200 <param name="batchmode_selector" value='optionSinglemode'/> 235 <param name="batchmode_selector" value='optionSinglemode' />
201 <param name="computeSampleNumber" value="1"/> 236 <param name="computeSampleNumber" value="1" />
202 </conditional> 237 </conditional>
203 <param name="pvalue" value='0.2'/> 238 <param name="pvalue" value='0.2' />
204 239
205 <conditional name="filter_conditional"> 240 <conditional name="filter_conditional">
206 <param name="filter_selector" value='optionXfold'/> 241 <param name="filter_selector" value='optionXfold' />
207 <param name="xfold" value='1.5'/> 242 <param name="xfold" value='1.5' />
208 </conditional> 243 </conditional>
209 244
210 <param name="backgroundModelFile" value="cHi-C/background.txt"/> 245 <param name="backgroundModelFile" value="cHi-C/background.txt" />
211 <param name="rangeUpstream" value="200000"/> 246 <param name="rangeUpstream" value="200000" />
212 <param name="rangeDownstream" value="200000"/> 247 <param name="rangeDownstream" value="200000" />
213 248
214 <output_collection name="significantFilesCollection" type="list" count="2"> 249 <output_collection name="significantFilesCollection" type="list" count="2">
215 <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"/> 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" />
216 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.txt" file="cHi-C/chicSignificantInteractions/output_3/MB-E10-5_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>
217 </output_collection> 259 </output_collection>
218
219 <output_collection name="targetFilesCollection" type="list" count="2"> 260 <output_collection name="targetFilesCollection" type="list" count="2">
220 <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"/> 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" />
221 <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"/> 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" />
222 </output_collection> 263 </output_collection>
223 </test> 264 </test>
224 265
225 <test> 266 <test>
226 <conditional name="tar_input_conditional"> 267 <conditional name="tar_input_conditional">
227 <param name="tar_input_selector" value='interval_input'/> 268 <param name="tar_input_selector" value='interval_input' />
228 <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"/> 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" />
229 </conditional> 270 </conditional>
230 <conditional name="batchmode_conditional"> 271 <conditional name="batchmode_conditional">
231 <param name="batchmode_selector" value='optionBatchmode'/> 272 <param name="batchmode_selector" value='optionBatchmode' />
232 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 273 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
233 <param name="computeSampleNumber" value='2'/> 274 <param name="computeSampleNumber" value='2' />
234 </conditional> 275 </conditional>
235 <param name="pvalue" value='0.2'/> 276 <param name="pvalue" value='0.2' />
236 277
237 <conditional name="filter_conditional"> 278 <conditional name="filter_conditional">
238 <param name="filter_selector" value='optionLoosePvalue'/> 279 <param name="filter_selector" value='optionLoosePvalue' />
239 <param name="loosePvalue" value='0.5'/> 280 <param name="loosePvalue" value='0.5' />
240 </conditional> 281 </conditional>
241 282
242 <param name="backgroundModelFile" value="cHi-C/background.txt"/> 283 <param name="backgroundModelFile" value="cHi-C/background.txt" />
243 <param name="rangeUpstream" value="200000"/> 284 <param name="rangeUpstream" value="200000" />
244 <param name="rangeDownstream" value="200000"/> 285 <param name="rangeDownstream" value="200000" />
245 286
246 <param name='tar' value='True'/> 287 <param name='tar' value='True' />
247 288
248 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> 289 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
249 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.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' />
250 291 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" />
251 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/> 292 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" />
252 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/>
253 </test> 293 </test>
254 294
255 <test> 295 <test>
256 <conditional name="tar_input_conditional"> 296 <conditional name="tar_input_conditional">
257 <param name="tar_input_selector" value='tar_input'/> 297 <param name="tar_input_selector" value='tar_input' />
258 <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar"/> 298 <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar" />
259 </conditional> 299 </conditional>
260 <conditional name="batchmode_conditional"> 300 <conditional name="batchmode_conditional">
261 <param name="batchmode_selector" value='optionBatchmode'/> 301 <param name="batchmode_selector" value='optionBatchmode' />
262 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 302 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt' />
263 <param name="computeSampleNumber" value='2'/> 303 <param name="computeSampleNumber" value='2' />
264 </conditional> 304 </conditional>
265 <param name="pvalue" value='0.2'/> 305 <param name="pvalue" value='0.2' />
266 306
267 <conditional name="filter_conditional"> 307 <conditional name="filter_conditional">
268 <param name="filter_selector" value='optionLoosePvalue'/> 308 <param name="filter_selector" value='optionLoosePvalue' />
269 <param name="loosePvalue" value='0.5'/> 309 <param name="loosePvalue" value='0.5' />
270 </conditional> 310 </conditional>
271 311
272 <param name="backgroundModelFile" value="cHi-C/background.txt"/> 312 <param name="backgroundModelFile" value="cHi-C/background.txt" />
273 <param name="rangeUpstream" value="200000"/> 313 <param name="rangeUpstream" value="200000" />
274 <param name="rangeDownstream" value="200000"/> 314 <param name="rangeDownstream" value="200000" />
275 315
276 <param name='tar' value='True'/> 316 <param name='tar' value='True' />
277 317
278 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' /> 318 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
279 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.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' />
280 320
281 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/> 321 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000' />
282 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.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' />
283 </test> 323 </test>
284
285 </tests> 324 </tests>
286 <help><![CDATA[ 325 <help><![CDATA[
287 326
288 Significant interaction detection 327 Significant interaction detection
289 ================================= 328 =================================
296 p-value based on the sum of interactions for this neighborhood is computed. Only interactions with a higher p-value as specified by the threshold `--pValue` are accepted as a significant interaction. 335 p-value based on the sum of interactions for this neighborhood is computed. Only interactions with a higher p-value as specified by the threshold `--pValue` are accepted as a significant interaction.
297 336
298 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 337 For more information about HiCExplorer please consider our documentation on readthedocs.io_
299 338
300 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 339 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
301 ]]></help> 340 ]]> </help>
302 <expand macro="citations" /> 341 <expand macro="citations" />
303 </tool> 342 </tool>