Mercurial > repos > iuc > hicexplorer_chicdifferentialtest

comparison chicDifferentialTest.xml @ 0:2468b1d3e832 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 9e4e8de0e003fc15f5bae3648232c2a8a57e6391"
author iuc
date Mon, 09 Dec 2019 10:29:32 +0000
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-1:000000000000 0:2468b1d3e832
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>