Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest

comparison chicDifferentialTest.xml @ 2:1e52af48d34e 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 17:10:43 -0400
parents fa6fc09ba259
children 126abc4b03f1
comparison
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1:7ec5229e2a19 2:1e52af48d34e
42 <option value="optionSinglemode" selected="True">Single file processing</option> 42 <option value="optionSinglemode" selected="True">Single file processing</option>
43 </param> 43 </param>
44 <when value="optionBatchmode"> 44 <when value="optionBatchmode">
45 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> 45 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
46 </when> 46 </when>
47 <when value="optionSinglemode"> 47 <when value="optionSinglemode">
48 </when> 48 </when>
49 </conditional> 49 </conditional>
50 <param name='alpha' type="float" value='2.0' label="Alpha" help='Accept all samples to significance level alpha.'/> 50 <param name='alpha' type="float" value='2.0' label="Alpha" help='Accept all samples to significance level alpha.'/>
51 <param name="statisticTest_selector" type="select" label="Statistical test"> 51 <param name="statisticTest_selector" type="select" label="Statistical test">
52 <option value="fisher" selected="True">Fisher exact</option> 52 <option value="fisher" selected="True">Fisher exact</option>
53 <option value="chi2">Chi2 contingency</option> 53 <option value="chi2">Chi2 contingency</option>
54 </param> 54 </param>
55 </inputs> 55 </inputs>
56 <outputs> 56 <outputs>
57 <collection name="differentialFolderCollection" type="list" label="Differential test files"> 57 <collection name="differentialFolderCollection" type="list" label="Differential test files">
58 <discover_datasets pattern="__name__" format="interval" directory="differentialFolder" /> 58 <discover_datasets pattern="__name__" format="interval" directory="differentialFolder" />
59 </collection> 59 </collection>
61 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> 61 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
62 </data> 62 </data>
63 </outputs> 63 </outputs>
64 <tests> 64 <tests>
65 <test> 65 <test>
66 <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.bed"/> 66 <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_aggregated.txt"/>
67 67
68 <conditional name="batchmode_conditional"> 68 <conditional name="batchmode_conditional">
69 <param name="batchmode_selector" value='optionBatchmode'/> 69 <param name="batchmode_selector" value='optionBatchmode'/>
70 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/> 70 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/>
71 </conditional> 71 </conditional>
72 <param name="statisticTest_selector" value='chi2'/> 72 <param name="statisticTest_selector" value='chi2'/>
73 <param name="alpha" value='0.5'/> 73 <param name="alpha" value='0.5'/>
74 <output_collection name="differentialFolderCollection" type="list" count="9"> 74 <output_collection name="differentialFolderCollection" type="list" count="9">
75 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed" ftype="interval" lines_diff="4"/> 75 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" ftype="interval" lines_diff="4"/>
76 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" ftype="interval" lines_diff="4"/> 76 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" ftype="interval" lines_diff="4"/>
77 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" ftype="interval" lines_diff="4"/> 77 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" ftype="interval" lines_diff="4"/>
78 78
79 79
80 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.bed" ftype="interval" lines_diff="4"/> 80 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_accepted.txt" ftype="interval" lines_diff="4"/>
81 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed" ftype="interval" lines_diff="4"/> 81 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.txt" ftype="interval" lines_diff="4"/>
82 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.bed" ftype="interval" lines_diff="4"/> 82 <element name="FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_results.txt" ftype="interval" lines_diff="4"/>
83 83
84 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.bed" ftype="interval" lines_diff="4"/> 84 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_accepted.txt" ftype="interval" lines_diff="4"/>
85 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed" ftype="interval" lines_diff="4"/> 85 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.txt" ftype="interval" lines_diff="4"/>
86 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.bed" ftype="interval" lines_diff="4"/> 86 <element name="FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt" file="cHi-C/chicDifferentialTest/batch_mode_chi2/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_results.txt" ftype="interval" lines_diff="4"/>
87 87
88 </output_collection> 88 </output_collection>
89 89
90 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/> 90 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/>
91 </test> 91 </test>
92 <test> 92 <test>
93 <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.bed"/> 93 <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt,cHi-C/chicAggregateStatistic/batch_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt"/>
94 94
95 <conditional name="batchmode_conditional"> 95 <conditional name="batchmode_conditional">
96 <param name="batchmode_selector" value='optionSinglemode'/> 96 <param name="batchmode_selector" value='optionSinglemode'/>
97 </conditional> 97 </conditional>
98 <param name="statisticTest_selector" value='fisher'/> 98 <param name="statisticTest_selector" value='fisher'/>
99 <param name="alpha" value='0.5'/> 99 <param name="alpha" value='0.5'/>
100 100
101 <output_collection name="differentialFolderCollection" type="list" count="3"> 101 <output_collection name="differentialFolderCollection" type="list" count="3">
102 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.bed" ftype="interval" lines_diff="4"/> 102 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_accepted.txt" ftype="interval" lines_diff="4"/>
103 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed" ftype="interval" lines_diff="4"/> 103 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.txt" ftype="interval" lines_diff="4"/>
104 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.bed" ftype="interval" lines_diff="4"/> 104 <element name="FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" file="cHi-C/chicDifferentialTest/regular_mode_fisher/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_results.txt" ftype="interval" lines_diff="4"/>
105 </output_collection> 105 </output_collection>
106 </test> 106 </test>
107 </tests> 107 </tests>
108 <help><![CDATA[ 108 <help><![CDATA[
109 109
110 Differential testing of two viewpoints 110 Differential testing of two viewpoints
111 ====================================== 111 ======================================
112 112
113 chicDifferentialTest tests if two locations under consideration of the reference point have a different interaction count. For this either Fisher's test or chi2 contingency test can be used. 113 chicDifferentialTest tests if two locations under consideration of the reference point have a different interaction count. Either Fisher's test or chi2 contingency test can be used.
114 The files that are accepted for this test can be created with `chicAggregateStatistic`. H0 is assuming the interactions are not different. Therefore the differential interaction counts are all where H0 was rejected. 114 Input files for this test can be created with `chicAggregateStatistic`. H0 is assuming the interactions are not different. Therefore the differential interaction counts are all where H0 was rejected.
115 115
116 116
117 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 117 For more information about HiCExplorer please consider our documentation on readthedocs.io_
118 118
119 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 119 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html