Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest

comparison chicDifferentialTest.xml @ 4:126abc4b03f1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author iuc
date Fri, 14 Aug 2020 06:15:21 -0400
parents 1e52af48d34e
children 975b6a67e4b0
comparison
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3:9180983da5c2 4:126abc4b03f1
1 <tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_chicdifferentialtest" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>computes differential interactions of viewpoints</description> 2 <description>computes differential interactions of viewpoints</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">chicDifferentialTest</token> 4 <token name="@BINARY@">chicDifferentialTest</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
9 #import re 9 #import re
10 10
11 mkdir interactionFiles && 11 mkdir interactionFiles &&
12 mkdir differentialFolder && 12 mkdir differentialFolder &&
13 13
14 #for $file in $interactionFiles: 14 #if $tar_input_conditional.tar_input_selector == 'tar_input':
15 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 15 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar &&
16 ln -s '$file' 'interactionFiles/$identifier' && 16 tar -C interactionFiles -xvf viewpoints.tar &&
17 #end for 17 #else:
18 18 #for $file in $tar_input_conditional.interactionFiles:
19 #set identifier = @ESCAPE_IDENTIFIER_FILE@
20
21 ln -s '$file' 'interactionFiles/$identifier' &&
22 #end for
23 #end if
19 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 24 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
20 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) 25 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
21 #end if 26 #end if
22 @BINARY@ 27 @BINARY@
23 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 28 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
30 #end if 35 #end if
31 --statisticTest $statisticTest_selector 36 --statisticTest $statisticTest_selector
32 --alpha $alpha 37 --alpha $alpha
33 --outputFolder differentialFolder 38 --outputFolder differentialFolder
34 --threads @THREADS@ 39 --threads @THREADS@
40
41 #if $tar:
42 && cd differentialFolder
43 && tar -cvf ../differentialFolder.tar *
44 && cd ..
45 && rm -rf differentialFolder
46 #end if
35 ]]></command> 47 ]]></command>
36 <inputs> 48 <inputs>
49 <conditional name="tar_input_conditional">
50 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
51 <option value="tar_input">tar file</option>
52 <option value="interval_input" selected="True">Interval files</option>
53 </param>
54 <when value="tar_input">
55 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
56 </when>
57 <when value="interval_input">
37 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 58 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
59 </when>
60 </conditional>
38 61
39 <conditional name="batchmode_conditional"> 62 <conditional name="batchmode_conditional">
40 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> 63 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
41 <option value="optionBatchmode">Batch processing</option> 64 <option value="optionBatchmode">Batch processing</option>
42 <option value="optionSinglemode" selected="True">Single file processing</option> 65 <option value="optionSinglemode" selected="True">Single file processing</option>
50 <param name='alpha' type="float" value='2.0' label="Alpha" help='Accept all samples to significance level alpha.'/> 73 <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"> 74 <param name="statisticTest_selector" type="select" label="Statistical test">
52 <option value="fisher" selected="True">Fisher exact</option> 75 <option value="fisher" selected="True">Fisher exact</option>
53 <option value="chi2">Chi2 contingency</option> 76 <option value="chi2">Chi2 contingency</option>
54 </param> 77 </param>
78 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
79 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
80
55 </inputs> 81 </inputs>
56 <outputs> 82 <outputs>
57 <collection name="differentialFolderCollection" type="list" label="Differential test files"> 83 <collection name="differentialFolderCollection" type="list" label="Differential test files">
58 <discover_datasets pattern="__name__" format="interval" directory="differentialFolder" /> 84 <discover_datasets pattern="__name__" format="interval" directory="differentialFolder" />
59 </collection> 85 </collection>
60 <data name="rejectedFileNames" from_work_dir="rejected_H0.txt" format="txt" label="${tool.name} rejected H0"> 86 <data name="rejectedFileNames" from_work_dir="rejected_H0.txt" format="txt" label="${tool.name} rejected H0">
61 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> 87 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
62 </data> 88 </data>
89 <data name="differentialFolderTar" from_work_dir="differentialFolder.tar" format="tar" label="Differential test files tar.gz">
90 <filter>tar</filter>
91 </data>
63 </outputs> 92 </outputs>
64 <tests> 93 <tests>
65 <test> 94 <test>
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"/> 95 <conditional name="tar_input_conditional">
96 <param name="tar_input_selector" value='interval_input'/>
97 <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"/>
98 </conditional>
67 99
68 <conditional name="batchmode_conditional"> 100 <conditional name="batchmode_conditional">
69 <param name="batchmode_selector" value='optionBatchmode'/> 101 <param name="batchmode_selector" value='optionBatchmode'/>
70 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/> 102 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/>
71 </conditional> 103 </conditional>
88 </output_collection> 120 </output_collection>
89 121
90 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/> 122 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/>
91 </test> 123 </test>
92 <test> 124 <test>
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"/> 125 <conditional name="tar_input_conditional">
126 <param name="tar_input_selector" value='interval_input'/>
127 <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"/>
128
129 </conditional>
94 130
95 <conditional name="batchmode_conditional"> 131 <conditional name="batchmode_conditional">
96 <param name="batchmode_selector" value='optionSinglemode'/> 132 <param name="batchmode_selector" value='optionSinglemode'/>
97 </conditional> 133 </conditional>
98 <param name="statisticTest_selector" value='fisher'/> 134 <param name="statisticTest_selector" value='fisher'/>
101 <output_collection name="differentialFolderCollection" type="list" count="3"> 137 <output_collection name="differentialFolderCollection" type="list" count="3">
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"/> 138 <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.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"/> 139 <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.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"/> 140 <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> 141 </output_collection>
142 </test>
143
144
145 <test>
146 <conditional name="tar_input_conditional">
147 <param name="tar_input_selector" value='interval_input'/>
148 <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"/>
149 </conditional>
150
151 <conditional name="batchmode_conditional">
152 <param name="batchmode_selector" value='optionBatchmode'/>
153 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/>
154 </conditional>
155 <param name="statisticTest_selector" value='chi2'/>
156 <param name="alpha" value='0.5'/>
157 <param name='tar' value='True'/>
158
159 <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype='tar' compare="sim_size" delta='40000' />
160
161 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/>
162 </test>
163
164 <test>
165 <conditional name="tar_input_conditional">
166 <param name="tar_input_selector" value='tar_input'/>
167 <param name="interactionFiles" value="cHi-C/chicAggregateStatistic/batch_mode.tar"/>
168 </conditional>
169
170 <conditional name="batchmode_conditional">
171 <param name="batchmode_selector" value='optionBatchmode'/>
172 <param name="interactionFilesOrderFile" value='cHi-C/chicAggregateStatistic/batch_mode_file_names.txt'/>
173 </conditional>
174 <param name="statisticTest_selector" value='chi2'/>
175 <param name="alpha" value='0.5'/>
176 <param name='tar' value='True'/>
177
178 <output name="differentialFolderTar" file="cHi-C/chicDifferentialTest/batch_mode_chi2.tar" ftype='tar' compare="sim_size" delta='40000' />
179
180 <output name="rejectedFileNames" file="cHi-C/chicDifferentialTest/rejectedFilesList.txt" ftype="txt" compare="sim_size" delta='40000'/>
106 </test> 181 </test>
107 </tests> 182 </tests>
108 <help><![CDATA[ 183 <help><![CDATA[
109 184
110 Differential testing of two viewpoints 185 Differential testing of two viewpoints