Mercurial > repos > bgruening > hicexplorer_chicsignificantinteractions

comparison chicSignificantInteractions.xml @ 4:38fa8a72ece6 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 05:59:38 -0400
parents 7668fac6cc3a
children 6001400eed99
comparison
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3:7668fac6cc3a 4:38fa8a72ece6
1 <tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_chicsignificantinteractions" name="@BINARY@" version="@WRAPPER_VERSION@.1">
2 <description>computes viewpoints with the given reference points and a background model</description> 2 <description>computes viewpoints with the given reference points and a background model</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">chicSignificantInteractions</token> 4 <token name="@BINARY@">chicSignificantInteractions</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
10 10
11 mkdir interactionFiles && 11 mkdir interactionFiles &&
12 mkdir targetFolder && 12 mkdir targetFolder &&
13 mkdir significantFilesFolder && 13 mkdir significantFilesFolder &&
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 17 tar -C interactionFiles -xvf viewpoints.tar &&
18 ln -s '$file' 'interactionFiles/$identifier' && 18 #else:
19 #end for 19 #for $file in $tar_input_conditional.interactionFiles:
20 20 #set identifier = @ESCAPE_IDENTIFIER_FILE@
21
22 ln -s '$file' 'interactionFiles/$identifier' &&
23 #end for
24 #end if
25
21 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 26 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
22 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ]) 27 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
23 #end if 28 #end if
24 @BINARY@ 29 @BINARY@
25 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode': 30 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
51 --outputFolder significantFilesFolder 56 --outputFolder significantFilesFolder
52 $truncateZeroPvalues 57 $truncateZeroPvalues
53 --fixateRange $fixateRange 58 --fixateRange $fixateRange
54 -suffix significant_interactions.txt 59 -suffix significant_interactions.txt
55 --threads @THREADS@ 60 --threads @THREADS@
61
62 #if $tar:
63 && cd targetFolder
64 && tar -cvf ../targetFolder.tar *
65 && cd ..
66 && rm -rf targetFolder
67
68 && cd significantFilesFolder
69 && tar -cvf ../significantFilesFolder.tar *
70 && cd ..
71 && rm -rf significantFilesFolder
72
73 #end if
56 ]]></command> 74 ]]></command>
57 <inputs> 75 <inputs>
76 <conditional name="tar_input_conditional">
77 <param name="tar_input_selector" type="select" label="Compute files individually or in batch mode">
78 <option value="tar_input">Tar file</option>
79 <option value="interval_input" selected="True">Interval files</option>
80 </param>
81 <when value="tar_input">
82 <param name='interactionFiles' type="data" format="tar" label="Interaction files" multiple="false"/>
83 </when>
84 <when value="interval_input">
58 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/> 85 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
86 </when>
87 </conditional>
88
89
90
59 <conditional name="batchmode_conditional"> 91 <conditional name="batchmode_conditional">
60 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode"> 92 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
61 <option value="optionBatchmode">Batch processing</option> 93 <option value="optionBatchmode">Batch processing</option>
62 <option value="optionSinglemode" selected="True">Single file processing</option> 94 <option value="optionSinglemode" selected="True">Single file processing</option>
63 </param> 95 </param>
94 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> 126 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
95 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' /> 127 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
96 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/> 128 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
97 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one." 129 <param name='truncateZeroPvalues' type='boolean' truevalue='--truncateZeroPvalues' falsevalue="" checked="false" label="Truncate zeros by setting them to one."
98 help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision."/> 130 help="Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not part of the significance decision."/>
131 <param name='tar' type='boolean' checked="false" truevalue='True' label="tar output to one file"
132 help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large."/>
99 </inputs> 133 </inputs>
100 <outputs> 134 <outputs>
101 <collection name="significantFilesCollection" type="list" label="Significant files"> 135 <collection name="significantFilesCollection" type="list" label="Significant files">
102 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" /> 136 <discover_datasets pattern="__name__" format="interval" directory="significantFilesFolder" />
103 </collection> 137 </collection>
108 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> 142 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
109 </data> 143 </data>
110 <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names"> 144 <data name="targetFileNames" from_work_dir="targetListFile.txt" format="txt" label="${tool.name} target file names">
111 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter> 145 <filter>batchmode_conditional.batchmode_selector == 'optionBatchmode'</filter>
112 </data> 146 </data>
147 <data name="targetFolderTar" from_work_dir="targetFolder.tar" format="tar" label="Target files tar">
148 <filter>tar</filter>
149 </data>
150 <data name="significantFilesFolderTar" from_work_dir="significantFilesFolder.tar" format="tar" label="Significant files tar">
151 <filter>tar</filter>
152 </data>
113 </outputs> 153 </outputs>
114 <tests> 154 <tests>
115 <test> 155 <test>
116 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/> 156 <conditional name="tar_input_conditional">
157 <param name="tar_input_selector" value='interval_input'/>
158 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
159 </conditional>
117 <conditional name="batchmode_conditional"> 160 <conditional name="batchmode_conditional">
118 <param name="batchmode_selector" value='optionBatchmode'/> 161 <param name="batchmode_selector" value='optionBatchmode'/>
119 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/> 162 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
120 <param name="computeSampleNumber" value='2'/> 163 <param name="computeSampleNumber" value='2'/>
121 </conditional> 164 </conditional>
147 </output_collection> 190 </output_collection>
148 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/> 191 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/>
149 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/> 192 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/>
150 </test> 193 </test>
151 <test> 194 <test>
152 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt"/> 195 <conditional name="tar_input_conditional">
196 <param name="tar_input_selector" value='interval_input'/>
197 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt"/>
198 </conditional>
153 <conditional name="batchmode_conditional"> 199 <conditional name="batchmode_conditional">
154 <param name="batchmode_selector" value='optionSinglemode'/> 200 <param name="batchmode_selector" value='optionSinglemode'/>
155 <param name="computeSampleNumber" value="1"/> 201 <param name="computeSampleNumber" value="1"/>
156 </conditional> 202 </conditional>
157 <param name="pvalue" value='0.2'/> 203 <param name="pvalue" value='0.2'/>
172 218
173 <output_collection name="targetFilesCollection" type="list" count="2"> 219 <output_collection name="targetFilesCollection" type="list" count="2">
174 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/> 220 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/>
175 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/> 221 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" file="cHi-C/chicSignificantInteractions/output_3_target/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_target.txt" ftype="interval" lines_diff="4"/>
176 </output_collection> 222 </output_collection>
223 </test>
224
225 <test>
226 <conditional name="tar_input_conditional">
227 <param name="tar_input_selector" value='interval_input'/>
228 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt,cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt,cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt"/>
229 </conditional>
230 <conditional name="batchmode_conditional">
231 <param name="batchmode_selector" value='optionBatchmode'/>
232 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
233 <param name="computeSampleNumber" value='2'/>
234 </conditional>
235 <param name="pvalue" value='0.2'/>
236
237 <conditional name="filter_conditional">
238 <param name="filter_selector" value='optionLoosePvalue'/>
239 <param name="loosePvalue" value='0.5'/>
240 </conditional>
241
242 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
243 <param name="rangeUpstream" value="200000"/>
244 <param name="rangeDownstream" value="200000"/>
245
246 <param name='tar' value='True'/>
247
248 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
249 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
250
251 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/>
252 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/>
253 </test>
254
255 <test>
256 <conditional name="tar_input_conditional">
257 <param name="tar_input_selector" value='tar_input'/>
258 <param name="interactionFiles" value="cHi-C/chicViewpoint/viewpoints.tar"/>
259 </conditional>
260 <conditional name="batchmode_conditional">
261 <param name="batchmode_selector" value='optionBatchmode'/>
262 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
263 <param name="computeSampleNumber" value='2'/>
264 </conditional>
265 <param name="pvalue" value='0.2'/>
266
267 <conditional name="filter_conditional">
268 <param name="filter_selector" value='optionLoosePvalue'/>
269 <param name="loosePvalue" value='0.5'/>
270 </conditional>
271
272 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
273 <param name="rangeUpstream" value="200000"/>
274 <param name="rangeDownstream" value="200000"/>
275
276 <param name='tar' value='True'/>
277
278 <output name="targetFolderTar" file="cHi-C/chicSignificantInteractions/targetFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
279 <output name="significantFilesFolderTar" file="cHi-C/chicSignificantInteractions/significantFilesFolder.tar" ftype='tar' compare="sim_size" delta='40000' />
280
281 <output name="targetFileNames" file="cHi-C/chicSignificantInteractions/output_5_target_list.txt" ftype="txt" compare="sim_size" delta='40000'/>
282 <output name="significantFileNames" file="cHi-C/chicSignificantInteractions/output_5_significant_files.txt" ftype="txt" compare="sim_size" delta='40000'/>
177 </test> 283 </test>
178 284
179 </tests> 285 </tests>
180 <help><![CDATA[ 286 <help><![CDATA[
181 287