Mercurial > repos > bgruening > hicexplorer_chicdifferentialtest
comparison chicDifferentialTest.xml @ 4:126abc4b03f1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit db84cc85222518217286b42262935edd3a49c98e"
author | iuc |
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date | Fri, 14 Aug 2020 06:15:21 -0400 |
parents | 1e52af48d34e |
children | 975b6a67e4b0 |
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3:9180983da5c2 | 4:126abc4b03f1 |
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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 |