Mercurial > repos > bgruening > hicexplorer_chicaggregatestatistic

comparison chicAggregateStatistic.xml @ 4:d6f5e51e97ec 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 06:19:12 -0400
parents fb981b15ccef
children b53973719d7b
comparison
equal deleted inserted replaced
3:63588847a75a 4:d6f5e51e97ec
1 <tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_chicaggregatestatistic" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>computes with a target file the to be tested regions for chicDifferentialTest</description> 2 <description>computes with a target file the to be tested regions for chicDifferentialTest</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">chicAggregateStatistic</token> 4 <token name="@BINARY@">chicAggregateStatistic</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
10 mkdir interactionFiles && 10 mkdir interactionFiles &&
11 mkdir targetFolder && 11 mkdir targetFolder &&
12 mkdir aggregatedFilesFolder && 12 mkdir aggregatedFilesFolder &&
13 13
14 14
15 #for $file in $interactionFiles: 15 #if $tar_input_conditional.tar_input_selector == 'tar_input':
16 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 16 ln -s '$tar_input_conditional.interactionFiles' viewpoints.tar &&
17 ln -s '$file' 'interactionFiles/$identifier' && 17 tar -C interactionFiles -xvf viewpoints.tar &&
18 #end for 18
19 19 #if $targetFiles:
20 #for $file in $targetFiles: 20 ln -s '$tar_input_conditional.targetFiles' targetFiles.tar &&
21 #set identifier = @ESCAPE_IDENTIFIER_FILE@ 21 tar -C targetFolder -xvf targetFiles.tar &&
22 ln -s '$file' 'targetFolder/$identifier' && 22 #end if
23 #end for 23 #else:
24 #for $file in $tar_input_conditional.interactionFiles:
25 #set identifier = @ESCAPE_IDENTIFIER_FILE@
26 ln -s '$file' 'interactionFiles/$identifier' &&
27 #end for
28
29 #for $file in $targetFiles:
30 #set identifier = @ESCAPE_IDENTIFIER_FILE@
31 ln -s '$file' 'targetFolder/$identifier' &&
32 #end for
33
34 #end if
35
24 36
25 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 37 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
26 #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) 38 #set $interactonfileslist = ' '.join([ 'interactionFiles/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
27 #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ]) 39 #set $targetfileslist = ' '.join([ 'targetFolder/%s' % @ESCAPE_IDENTIFIER_FILE@ for $file in $targetFiles ])
28 40
42 54
43 --outputFolder aggregatedFilesFolder 55 --outputFolder aggregatedFilesFolder
44 -suffix aggregated.txt 56 -suffix aggregated.txt
45 --threads @THREADS@ 57 --threads @THREADS@
46 58
59 #if $tar:
60 && cd aggregatedFilesFolder
61 && tar -cvf ../aggregatedFilesFolder.tar *
62 && cd ..
63 && rm -rf aggregatedFilesFolder
64 #end if
65
47 ]]></command> 66 ]]></command>
48 <inputs> 67 <inputs>
49 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 68
50 <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/> 69 <conditional name="tar_input_conditional">
70 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
71 <option value="tar_input">Tar file</option>
72 <option value="interval_input" selected="True">Interval files</option>
73 </param>
74 <when value="tar_input">
75 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
76 <param name='targetFiles' type="data" format="tar" label="Target files" multiple="false"/>
77 </when>
78 <when value="interval_input">
79 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
80 <param name='targetFiles' type="data" format="interval" label="Target files" multiple="true"/>
81 </when>
82 </conditional>
83
51 84
52 <conditional name="batchmode_conditional"> 85 <conditional name="batchmode_conditional">
53 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> 86 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
54 <option value="optionBatchmode">Batch processing</option> 87 <option value="optionBatchmode">Batch processing</option>
55 <option value="optionSinglemode" selected="True">Single file processing</option> 88 <option value="optionSinglemode" selected="True">Single file processing</option>
60 93
61 </when> 94 </when>
62 <when value="optionSinglemode"> 95 <when value="optionSinglemode">
63 </when> 96 </when>
64 </conditional> 97 </conditional>
98 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
99 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
100
65 </inputs> 101 </inputs>
66 <outputs> 102 <outputs>
67 <collection name="aggregatedFilesCollection" type="list" label="Aggregated files"> 103 <collection name="aggregatedFilesCollection" type="list" label="Aggregated files">
104
68 <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" /> 105 <discover_datasets pattern="__name__" format='interval' directory="aggregatedFilesFolder" />
69 </collection> 106 </collection>
70 <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names"> 107 <data name="aggregatedFileNames" from_work_dir="aggregatedFilesBatch.txt" format="txt" label="${tool.name} aggregated file names">
71 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> 108 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
109 </data>
110 <data name="aggregatedFilesFolderTar" from_work_dir="aggregatedFilesFolder.tar" format="tar" label="Aggregated files tar.gz">
111 <filter>tar</filter>
72 </data> 112 </data>
73 </outputs> 113 </outputs>
74 <tests> 114 <tests>
75 <test> 115 <test>
76 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/> 116 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
106 <output_collection name="aggregatedFilesCollection" type="list" count="2"> 146 <output_collection name="aggregatedFilesCollection" type="list" count="2">
107 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/> 147 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
108 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/> 148 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" file="cHi-C/chicAggregateStatistic/regular_mode/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_aggregated.txt" ftype="interval" lines_diff="4"/>
109 </output_collection> 149 </output_collection>
110 </test> 150 </test>
151
152 <test>
153 <conditional name="tar_input_conditional">
154 <param name="tar_input_selector" value='interval_input'/>
155 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
156 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt,cHi-C/chicSignificantInteractions/output_5_target/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_target.txt"/>
157 </conditional>
158
159 <conditional name="batchmode_conditional">
160 <param name="batchmode_selector" value='optionBatchmode'/>
161 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
162 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
163 </conditional>
164
165 <param name='tar' value='True'/>
166
167 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
168 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
169 </test>
170
171 <test>
172 <conditional name="tar_input_conditional">
173 <param name="tar_input_selector" value='tar_input'/>
174 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1.tar"/>
175 <param name="targetFiles" value="cHi-C/chicSignificantInteractions/targetFolder.tar"/>
176 </conditional>
177
178 <conditional name="batchmode_conditional">
179 <param name="batchmode_selector" value='optionBatchmode'/>
180 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
181 <param name="targetFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_target_list.txt'/>
182 </conditional>
183
184 <param name='tar' value='True'/>
185
186 <output name="aggregatedFilesFolderTar" file="cHi-C/chicAggregateStatistic/batch_mode.tar" ftype='tar' compare="sim_size" delta='40000' />
187 <output name="aggregatedFileNames" file="cHi-C/chicAggregateStatistic/batch_mode_file_names.txt" ftype="txt" compare="sim_size" delta='40000'/>
188 </test>
111 </tests> 189 </tests>
112 <help><![CDATA[ 190 <help><![CDATA[
113 191
114 Aggregate statistic for differential testing 192 Aggregate statistic for differential testing
115 ============================================ 193 ============================================