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comparison chicSignificantInteractions.xml @ 0:2f279a01f3ff draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:37:16 -0500
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children 1db84db797b1
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-1:000000000000 0:2f279a01f3ff
1 <tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>computes viewpoints with the given reference points and a background model</description>
3 <macros>
4 <token name="@BINARY@">chicSignificantInteractions</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10
11 mkdir interactionFiles &&
12 mkdir targetFolder &&
13 mkdir significantFilesFolder &&
14
15 #for $file in $interactionFiles:
16 #set identifier = @ESCAPE_IDENTIFIER_FILE@
17
18 ln -s '$file' 'interactionFiles/$identifier' &&
19 #end for
20
21 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
22 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
23 #end if
24 @BINARY@
25 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
26 --interactionFile $interactonfileslist
27 --computeSampleNumber $batchmode_conditional.computeSampleNumber
28
29 #else:
30 --interactionFile $batchmode_conditional.interactionFilesOrderFile
31 --interactionFileFolder interactionFiles
32 --batchMode
33 --targetFileList targetListFile.txt
34 --writeFileNamesToFile significantFiles.txt
35 --computeSampleNumber $batchmode_conditional.computeSampleNumber
36 #end if
37
38 --pValue $pvalue
39
40 #if $filter_conditional.filter_selector == 'optionXfold':
41 --xFoldBackground $filter_conditional.xfold
42 #else:
43 --loosePValue $filter_conditional.loosePvalue
44
45 #end if
46 --backgroundModelFile '$backgroundModelFile'
47 --resolution $resolution
48 --peakInteractionsThreshold $peakInteractionsThreshold
49 --range $rangeUpstream $rangeDownstream
50 --targetFolder targetFolder
51 --outputFolder significantFilesFolder
52
53 --xFoldMaxValueNB $xFoldMaxValueNB
54 --fixateRange $fixateRange
55 -suffix significant_interactions.bed
56 --threads @THREADS@
57 ]]></command>
58 <inputs>
59 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
60 <conditional name="batchmode_conditional">
61 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
62 <option value="optionBatchmode">Batch processing</option>
63 <option value="optionSinglemode" selected="True">Single file processing</option>
64 </param>
65 <when value="optionBatchmode">
66 <param name='interactionFilesOrderFile' type="data" format="interval" label="Interaction file order"/>
67 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/>
68 </when>
69 <when value="optionSinglemode">
70 <param name='computeSampleNumber' type="integer" value='2' label="Create one target file for n consecutive files."/>
71 </when>
72 </conditional>
73 <param name='pvalue' type="float" value='0.05' label="P-value of interaction to be accepted as significant"/>
74 <conditional name="filter_conditional">
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>
77 <option value="optionLoosePvalue" selected="True">Loose p-value (NB background)</option>
78 </param>
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
81 less significant interactions to one peak with high significance. Used only for pValue option.'/>
82 </when>
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.
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.'/>
87 </when>
88 </conditional>
89 <param argument="--backgroundModelFile" type="data" format='tabular'
90 label="Background model"
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.'/>
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.'/>
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.' />
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.'/>
99 </inputs>
100 <outputs>
101 <collection name="significantFilesCollection" type="list" label="Significant files">
102 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" />
103 </collection>
104 <collection name="targetFilesCollection" type="list" label="Target files">
105 <discover_datasets pattern="__name__" format="interval" directory="targetFolder" />
106 </collection>
107 <data name="significantFileNames" from_work_dir="significantFiles.txt" format="txt" label="${tool.name} significant file names">
108 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
109 </data>
110 <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names">
111 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
112 </data>
113 </outputs>
114 <tests>
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"/>
117 <conditional name="batchmode_conditional">
118 <param name="batchmode_selector" value='optionBatchmode'/>
119 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
120 <param name="computeSampleNumber" value='2'/>
121 </conditional>
122 <param name="pvalue" value='0.2'/>
123
124 <conditional name="filter_conditional">
125 <param name="filter_selector" value='optionLoosePvalue'/>
126 <param name="loosePvalue" value='0.5'/>
127 </conditional>
128
129 <param name="backgroundModelFile" value="cHi-C/background.bed"/>
130 <param name="rangeUpstream" value="200000"/>
131 <param name="rangeDownstream" value="200000"/>
132
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"/>
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"/>
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"/>
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"/>
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"/>
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"/>
141 </output_collection>
142
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"/>
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"/>
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"/>
147 </output_collection>
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'/>
150 </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"/>
153 <conditional name="batchmode_conditional">
154 <param name="batchmode_selector" value='optionSinglemode'/>
155 <param name="computeSampleNumber" value="1"/>
156 </conditional>
157 <param name="pvalue" value='0.2'/>
158
159 <conditional name="filter_conditional">
160 <param name="filter_selector" value='optionXfold'/>
161 <param name="xfold" value='1.5'/>
162 </conditional>
163
164 <param name="backgroundModelFile" value="cHi-C/background.bed"/>
165 <param name="rangeUpstream" value="200000"/>
166 <param name="rangeDownstream" value="200000"/>
167
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"/>
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"/>
171 </output_collection>
172
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"/>
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"/>
176 </output_collection>
177 </test>
178
179 </tests>
180 <help><![CDATA[
181
182 Significant interaction detection
183 =================================
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
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
187 to test for a differential interaction scheme.
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
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
192 For more information about HiCExplorer please consider our documentation on readthedocs.io_
193
194 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
195 ]]></help>
196 <expand macro="citations" />
197 </tool>