Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions

comparison chicSignificantInteractions.xml @ 2:3df84bb4486c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 16:54:59 -0400
parents 1db84db797b1
children 7668fac6cc3a
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1:1db84db797b1 2:3df84bb4486c
32 --batchMode 32 --batchMode
33 --targetFileList targetListFile.txt 33 --targetFileList targetListFile.txt
34 --writeFileNamesToFile significantFiles.txt 34 --writeFileNamesToFile significantFiles.txt
35 --computeSampleNumber $batchmode_conditional.computeSampleNumber 35 --computeSampleNumber $batchmode_conditional.computeSampleNumber
36 #end if 36 #end if
37 37
38 --pValue $pvalue 38 --pValue $pvalue
39 39
40 #if $filter_conditional.filter_selector == 'optionXfold': 40 #if $filter_conditional.filter_selector == 'optionXfold':
41 --xFoldBackground $filter_conditional.xfold 41 --xFoldBackground $filter_conditional.xfold
42 #else: 42 #else:
50 --targetFolder targetFolder 50 --targetFolder targetFolder
51 --outputFolder significantFilesFolder 51 --outputFolder significantFilesFolder
52 52
53 --xFoldMaxValueNB $xFoldMaxValueNB 53 --xFoldMaxValueNB $xFoldMaxValueNB
54 --fixateRange $fixateRange 54 --fixateRange $fixateRange
55 -suffix significant_interactions.bed 55 -suffix significant_interactions.txt
56 --threads @THREADS@ 56 --threads @THREADS@
57 ]]></command> 57 ]]></command>
58 <inputs> 58 <inputs>
59 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 59 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
60 <conditional name="batchmode_conditional"> 60 <conditional name="batchmode_conditional">
61 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> 61 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
62 <option value="optionBatchmode">Batch processing</option> 62 <option value="optionBatchmode">Batch processing</option>
63 <option value="optionSinglemode" selected="True">Single file processing</option> 63 <option value="optionSinglemode" selected="True">Single file processing</option>
64 </param> 64 </param>
65 <when value="optionBatchmode"> 65 <when value="optionBatchmode">
66 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> 66 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
67 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/> 67 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/>
68 </when> 68 </when>
69 <when value="optionSinglemode"> 69 <when value="optionSinglemode">
70 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/> 70 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/>
71 </when> 71 </when>
72 </conditional> 72 </conditional>
73 <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant"/> 73 <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant"/>
74 <conditional name="filter_conditional"> 74 <conditional name="filter_conditional">
75 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions"> 75 <param name="filter_selector" type="select" label="List of chromosomes or a BED file containg regions">
76 <option value="optionXfold">x-fold over mean background</option> 76 <option value="optionXfold">x-fold over mean background</option>
77 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option> 77 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option>
78 </param> 78 </param>
79 <when value="optionXfold"> 79 <when value="optionXfold">
80 <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 80 <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
81 less significant interactions to one peak with high significance. Used only for pValue option.'/> 81 less significant interactions to one peak with high significance. Used only for pValue option.'/>
82 </when> 82 </when>
83 <when value="optionLoosePvalue"> 83 <when value="optionLoosePvalue">
84 <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. 84 <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.
85 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance. 85 Used to merge neighboring bins with a broader peak but less significant interactions to one peak with high significance.
86 Used only for pValue option.'/> 86 Used only for pValue option.'/>
87 </when> 87 </when>
88 </conditional> 88 </conditional>
89 <param argument="--backgroundModelFile" type="data" format='tabular' 89 <param argument="--backgroundModelFile" type="data" format='tabular'
90 label="Background model" 90 label="Background model"
91 help="The background file computed by chicViewpointBackgroundModel" /> 91 help="The background file computed by chicViewpointBackgroundModel" />
92 <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.'/> 92 <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.'/>
93 <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. 93 <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.
94 This value is used to merge neighboring bins.'/> 94 This value is used to merge neighboring bins.'/>
95 <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.' /> 95 <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.' />
96 <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.' /> 96 <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.' />
97 <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.'/> 97 <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.'/>
98 <param argument="--xFoldMaxValueNB" type="integer" value="10" label="x-fold for NB distributions" help='x-fold factor to increase the number of precomputed p-values per relative genomic distance. If set to 1, the maximal distance is used.'/> 98 <param argument="--xFoldMaxValueNB" type="integer" value="10" label="x-fold for NB distributions" help='x-fold factor to increase the number of precomputed p-values per relative genomic distance. If set to 1, the maximal distance is used.'/>
99 </inputs> 99 </inputs>
100 <outputs> 100 <outputs>
101 <collection name="significantFilesCollection" type="list" label="Significant files"> 101 <collection name="significantFilesCollection" type="list" label="Significant files">
102 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" /> 102 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" />
103 </collection> 103 </collection>
111 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> 111 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
112 </data> 112 </data>
113 </outputs> 113 </outputs>
114 <tests> 114 <tests>
115 <test> 115 <test>
116 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed"/> 116 <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"/>
117 <conditional name="batchmode_conditional"> 117 <conditional name="batchmode_conditional">
118 <param name="batchmode_selector" value='optionBatchmode'/> 118 <param name="batchmode_selector" value='optionBatchmode'/>
119 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 119 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
120 <param name="computeSampleNumber" value='2'/> 120 <param name="computeSampleNumber" value='2'/>
121 </conditional> 121 </conditional>
124 <conditional name="filter_conditional"> 124 <conditional name="filter_conditional">
125 <param name="filter_selector" value='optionLoosePvalue'/> 125 <param name="filter_selector" value='optionLoosePvalue'/>
126 <param name="loosePvalue" value='0.5'/> 126 <param name="loosePvalue" value='0.5'/>
127 </conditional> 127 </conditional>
128 128
129 <param name="backgroundModelFile" value="cHi-C/background.bed"/> 129 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
130 <param name="rangeUpstream" value="200000"/> 130 <param name="rangeUpstream" value="200000"/>
131 <param name="rangeDownstream" value="200000"/> 131 <param name="rangeDownstream" value="200000"/>
132 132
133 <output_collection name="significantFilesCollection" type="list" count="6"> 133 <output_collection name="significantFilesCollection" type="list" count="6">
134 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.bed" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed" ftype="interval" lines_diff="4"/> 134 <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_output_significant.txt" ftype="interval" lines_diff="4"/>
135 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.bed" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed" ftype="interval" lines_diff="4"/> 135 <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_output_significant.txt" ftype="interval" lines_diff="4"/>
136 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.bed" file="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed" ftype="interval" lines_diff="4"/> 136 <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_output_significant.txt" ftype="interval" lines_diff="4"/>
137 137
138 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17_significant_interactions.bed" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed" ftype="interval" lines_diff="4"/> 138 <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_output_significant.txt" ftype="interval" lines_diff="4"/>
139 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.bed" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed" ftype="interval" lines_diff="4"/> 139 <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_output_significant.txt" ftype="interval" lines_diff="4"/>
140 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_significant_interactions.bed" file="cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed" ftype="interval" lines_diff="4"/> 140 <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_output_significant.txt" ftype="interval" lines_diff="4"/>
141 </output_collection> 141 </output_collection>
142 142
143 <output_collection name="targetFilesCollection" type="list" count="3"> 143 <output_collection name="targetFilesCollection" type="list" count="3">
144 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.bed" ftype="interval" lines_diff="4"/> 144 <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"/>
145 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed" ftype="interval" lines_diff="4"/> 145 <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"/>
146 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed" file="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.bed" ftype="interval" lines_diff="4"/> 146 <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"/>
147 </output_collection> 147 </output_collection>
148 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/> 148 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/>
149 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/> 149 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/>
150 </test> 150 </test>
151 <test> 151 <test>
152 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed"/> 152 <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"/>
153 <conditional name="batchmode_conditional"> 153 <conditional name="batchmode_conditional">
154 <param name="batchmode_selector" value='optionSinglemode'/> 154 <param name="batchmode_selector" value='optionSinglemode'/>
155 <param name="computeSampleNumber" value="1"/> 155 <param name="computeSampleNumber" value="1"/>
156 </conditional> 156 </conditional>
157 <param name="pvalue" value='0.2'/> 157 <param name="pvalue" value='0.2'/>
159 <conditional name="filter_conditional"> 159 <conditional name="filter_conditional">
160 <param name="filter_selector" value='optionXfold'/> 160 <param name="filter_selector" value='optionXfold'/>
161 <param name="xfold" value='1.5'/> 161 <param name="xfold" value='1.5'/>
162 </conditional> 162 </conditional>
163 163
164 <param name="backgroundModelFile" value="cHi-C/background.bed"/> 164 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
165 <param name="rangeUpstream" value="200000"/> 165 <param name="rangeUpstream" value="200000"/>
166 <param name="rangeDownstream" value="200000"/> 166 <param name="rangeDownstream" value="200000"/>
167 167
168 <output_collection name="significantFilesCollection" type="list" count="2"> 168 <output_collection name="significantFilesCollection" type="list" count="2">
169 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.bed" file="cHi-C/chicSignificantInteractions/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed" ftype="interval" lines_diff="4"/> 169 <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"/>
170 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_significant_interactions.bed" file="cHi-C/chicSignificantInteractions/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed" ftype="interval" lines_diff="4"/> 170 <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"/>
171 </output_collection> 171 </output_collection>
172 172
173 <output_collection name="targetFilesCollection" type="list" count="2"> 173 <output_collection name="targetFilesCollection" type="list" count="2">
174 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed" file="cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.bed" ftype="interval" lines_diff="4"/> 174 <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"/>
175 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed" file="cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.bed" ftype="interval" lines_diff="4"/> 175 <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"/>
176 </output_collection> 176 </output_collection>
177 </test> 177 </test>
178 178
179 </tests> 179 </tests>
180 <help><![CDATA[ 180 <help><![CDATA[
181 181
182 Significant interaction detection 182 Significant interaction detection
183 ================================= 183 =================================
184 184
185 Per viewpoint the significant interactions are detected based on the background model. Each viewpoint file gets as output a file with all recorded significant interactions and 185 Significant interactions are detected by this tool for each viewpoint based on the background model. chicSignificantInteractions outputs for each viewpoint a file containing all recorded significant interactions and
186 a target file. The target file is especially in the batch mode context useful, it merges for two consecutive listed control and treatment viewpoint the significant interactions which can then be used 186 a target file. The target file is especially useful in the batch mode context, as it merges for two consecutive listed control and treatment viewpoint the significant interactions which can then be used
187 to test for a differential interaction scheme. 187 to test for a differential interaction scheme.
188 188
189 chicSignificantInteractions supports two modes to detect significant interactions, either by an x-fold over the average background or a loose p-value. In both cases neighboring significant peaks are merged together and an additional 189 chicSignificantInteractions supports two modes to detect significant interactions, either by an x-fold over the average background or a loose p-value. In both cases neighboring significant peaks are merged together and an additional
190 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. 190 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.
191 191