Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest
comparison chicDifferentialTest.xml @ 0:fa6fc09ba259 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author | bgruening |
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date | Mon, 16 Dec 2019 14:36:01 -0500 |
parents | |
children | 1e52af48d34e |
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-1:000000000000 | 0:fa6fc09ba259 |
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1 <tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | |
2 <description>computes differential interactions of viewpoints</description> | |
3 <macros> | |
4 <token name="@BINARY@">chicDifferentialTest</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 differentialFolder && | |
13 | |
14 #for $file in $interactionFiles: | |
15 #set identifier = @ESCAPE_IDENTIFIER_FILE@ | |
16 ln -s '$file' 'interactionFiles/$identifier' && | |
17 #end for | |
18 | |
19 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': | |
20 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) | |
21 #end if | |
22 @BINARY@ | |
23 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': | |
24 --interactionFile $interactonfileslist | |
25 #else: | |
26 --interactionFile $batchmode_conditional.interactionFilesOrderFile | |
27 --interactionFileFolder interactionFiles | |
28 --batchMode | |
29 --rejectedFileNamesToFile rejected_H0.txt | |
30 #end if | |
31 --statisticTest $statisticTest_selector | |
32 --alpha $alpha | |
33 --outputFolder differentialFolder | |
34 --threads @THREADS@ | |
35 ]]></command> | |
36 <inputs> | |
37 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> | |
38 | |
39 <conditional name="batchmode_conditional"> | |
40 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> | |
41 <option value="optionBatchmode">Batch processing</option> | |
42 <option value="optionSinglemode" selected="True">Single file processing</option> | |
43 </param> | |
44 <when value="optionBatchmode"> | |
45 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/> | |
46 </when> | |
47 <when value="optionSinglemode"> | |
48 </when> | |
49 </conditional> | |
50 <param name='alpha' type="float" value='2.0' label="Alpha" help='Accept all samples to significance level alpha.'/> | |
51 <param name="statisticTest_selector" type="select" label="Statistical test"> | |
52 <option value="fisher" selected="True">Fisher exact</option> | |
53 <option value="chi2">Chi2 contingency</option> | |
54 </param> | |
55 </inputs> | |
56 <outputs> | |
57 <collection name="differentialFolderCollection" type="list" label="Differential test files"> | |
58 <discover_datasets pattern="__name__" format="interval" directory="differentialFolder" /> | |
59 </collection> | |
60 <data name="rejectedFileNames" from_work_dir="rejected_H0.txt" format="txt" label="${tool.name} rejected H0"> | |
61 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> | |
62 </data> | |
63 </outputs> | |
64 <tests> | |
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"/> | |
67 | |
68 <conditional name="batchmode_conditional"> | |
69 <param name="batchmode_selector" value='optionBatchmode'/> | |
70 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/> | |
71 </conditional> | |
72 <param name="statisticTest_selector" value='chi2'/> | |
73 <param name="alpha" value='0.5'/> | |
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"/> | |
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"/> | |
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"/> | |
78 | |
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"/> | |
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"/> | |
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"/> | |
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"/> | |
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"/> | |
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"/> | |
87 | |
88 </output_collection> | |
89 | |
90 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/> | |
91 </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"/> | |
94 | |
95 <conditional name="batchmode_conditional"> | |
96 <param name="batchmode_selector" value='optionSinglemode'/> | |
97 </conditional> | |
98 <param name="statisticTest_selector" value='fisher'/> | |
99 <param name="alpha" value='0.5'/> | |
100 | |
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"/> | |
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"/> | |
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"/> | |
105 </output_collection> | |
106 </test> | |
107 </tests> | |
108 <help><![CDATA[ | |
109 | |
110 Differential testing of two viewpoints | |
111 ====================================== | |
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. | |
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. | |
115 | |
116 | |
117 For more information about HiCExplorer please consider our documentation on readthedocs.io_ | |
118 | |
119 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | |
120 ]]></help> | |
121 <expand macro="citations" /> | |
122 </tool> |