Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest

comparison chicDifferentialTest.xml @ 8:9d42a6133690 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:23:20 +0000
parents 975b6a67e4b0
children 57aeaf6b237d
comparison
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7:9d878ac82c0f 8:9d42a6133690
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #import re 9 #import re
10
11 mkdir interactionFiles &&
12 mkdir differentialFolder &&
13
14 #if $tar_input_conditional.tar_input_selector == 'tar_input':
15 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar &&
16 tar -C interactionFiles -xvf viewpoints.tar &&
17 #else:
18 #for $file in $tar_input_conditional.interactionFiles:
19 #set identifier = @ESCAPE_IDENTIFIER_FILE@
20 ln -s '$file' 'interactionFiles/$identifier' &&
21 #end for
22 #end if
23 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
24 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
25 #end if
26 @BINARY@ 10 @BINARY@
27 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 11 --aggregatedFile $aggregatedFile
28 --interactionFile $interactonfileslist
29 #else:
30 --interactionFile $batchmode_conditional.interactionFilesOrderFile
31 --interactionFileFolder interactionFiles
32 --batchMode
33 --rejectedFileNamesToFile rejected_H0.txt
34 #end if
35 --statisticTest $statisticTest_selector 12 --statisticTest $statisticTest_selector
36 --alpha $alpha 13 --alpha $alpha
37 --outputFolder differentialFolder 14 --outFileName differentialFile.hdf5
38 --threads @THREADS@ 15 --threads @THREADS@
39 16
40 #if $tar:
41 && cd differentialFolder
42 && tar -cvf ../differentialFolder.tar *
43 && cd ..
44 && rm -rf differentialFolder
45 #end if
46 ]]> </command> 17 ]]> </command>
47 <inputs> 18 <inputs>
48 <conditional name="tar_input_conditional"> 19 <param name="aggregatedFile" type="data" format="h5" label="The aggregated data file created by chicAggregateStatistic" />
49 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode"> 20 <param name="alpha" type="float" value="2.0" label="Alpha" help="Accept all samples to significance level alpha." />
50 <option value="tar_input">tar file</option>
51 <option value="interval_input" selected="True">Interval files</option>
52 </param>
53 <when value="tar_input">
54 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false" />
55 </when>
56 <when value="interval_input">
57 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true" />
58 </when>
59 </conditional>
60
61 <conditional name="batchmode_conditional">
62 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
63 <option value="optionBatchmode">Batch processing</option>
64 <option value="optionSinglemode" selected="True">Single file processing</option>
65 </param>
66 <when value="optionBatchmode">
67 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order" />
68 </when>
69 <when value="optionSinglemode">
70 </when>
71 </conditional>
72 <param name='alpha' type="float" value='2.0' label="Alpha" help='Accept all samples to significance level alpha.' />
73 <param name="statisticTest_selector" type="select" label="Statistical test"> 21 <param name="statisticTest_selector" type="select" label="Statistical test">
74 <option value="fisher" selected="True">Fisher exact</option> 22 <option value="fisher" selected="True">Fisher exact</option>
75 <option value="chi2">Chi2 contingency</option> 23 <option value="chi2">Chi2 contingency</option>
76 </param> 24 </param>
77 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file" help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large." />
78
79 </inputs> 25 </inputs>
80 <outputs> 26 <outputs>
81 <collection name="differentialFolderCollection" type="list" label="Differential test files"> 27 <data name="differentialFile" from_work_dir="differentialFile.hdf5" format="h5" label="Differential test file" />
82 <discover_datasets pattern="__name__" format="interval" directory="differentialFolder" />
83 </collection>
84 <data name="rejectedFileNames" from_work_dir="rejected_H0.txt" format="txt" label="${tool.name} rejected H0">
85 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
86 </data>
87 <data name="differentialFolderTar" from_work_dir="differentialFolder.tar" format="tar" label="Differential test files tar.gz">
88 <filter>tar</filter>
89 </data>
90 </outputs> 28 </outputs>
91 <tests> 29 <tests>
92 <test> 30 <test>
93 <conditional name="tar_input_conditional"> 31 <param name="aggregatedFile" value="cHi-C/chicAggregateStatistic/aggregate.hdf5" />
94 <param name="tar_input_selector" value='interval_input' /> 32 <param name="statisticTest_selector" value="chi2" />
95 <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" /> 33 <param name="alpha" value="0.5" />
96 </conditional> 34 <output name="differentialFile" ftype="h5">
97 35 <assert_contents>
98 <conditional name="batchmode_conditional"> 36 <has_h5_attribute key="type" value="differential" />
99 <param name="batchmode_selector" value='optionBatchmode' /> 37 </assert_contents>
100 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt' /> 38 </output>
101 </conditional>
102 <param name="statisticTest_selector" value='chi2' />
103 <param name="alpha" value='0.5' />
104 <output_collection name="differentialFolderCollection" type="list" count="9">
105 <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" />
106 <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" />
107 <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" />
108 <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" />
109 <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" />
110 <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" />
111 <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" />
112 <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" />
113 <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" />
114 </output_collection>
115
116 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000' />
117 </test>
118 <test>
119 <conditional name="tar_input_conditional">
120 <param name="tar_input_selector" value='interval_input' />
121 <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" />
122 </conditional>
123 <conditional name="batchmode_conditional">
124 <param name="batchmode_selector" value='optionSinglemode' />
125 </conditional>
126 <param name="statisticTest_selector" value='fisher' />
127 <param name="alpha" value='0.5' />
128 <output_collection name="differentialFolderCollection" type="list" count="3">
129 <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" />
130 <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" />
131 <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" />
132 </output_collection>
133 </test>
134 <test>
135 <conditional name="tar_input_conditional">
136 <param name="tar_input_selector" value='interval_input' />
137 <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" />
138 </conditional>
139
140 <conditional name="batchmode_conditional">
141 <param name="batchmode_selector" value='optionBatchmode' />
142 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt' />
143 </conditional>
144 <param name="statisticTest_selector" value='chi2' />
145 <param name="alpha" value='0.5' />
146 <param name='tar' value='True' />
147 <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype='tar' compare="sim_size" delta='40000' />
148 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" />
149 </test>
150
151 <test>
152 <conditional name="tar_input_conditional">
153 <param name="tar_input_selector" value='tar_input' />
154 <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode.tar" />
155 </conditional>
156
157 <conditional name="batchmode_conditional">
158 <param name="batchmode_selector" value='optionBatchmode' />
159 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt' />
160 </conditional>
161 <param name="statisticTest_selector" value='chi2' />
162 <param name="alpha" value='0.5' />
163 <param name='tar' value='True' />
164 <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype='tar' compare="sim_size" delta='40000' />
165 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" />
166 </test> 39 </test>
167 </tests> 40 </tests>
168 <help><![CDATA[ 41 <help><![CDATA[
169 42
170 Differential testing of two viewpoints 43 Differential testing of two viewpoints