Mercurial > repos > bgruening > hicexplorer_chicplotviewpoint

comparison chicPlotViewpoint.xml @ 0:ae8bf5420df2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author bgruening
date Mon, 16 Dec 2019 15:40:31 -0500
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children 136ebddd6ec3
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-1:000000000000 0:ae8bf5420df2
1 <tool id="hicexplorer_chicplotviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>creates plots for viewpoints</description>
3 <macros>
4 <token name="@BINARY@">chicPlotViewpoint</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10
11 mkdir interactionFiles &&
12 mkdir differentialFolder &&
13 mkdir significantFolder &&
14 mkdir plots &&
15
16
17 #for $file in $interactionFiles:
18 #set identifier = @ESCAPE_IDENTIFIER_FILE@
19 ln -s '$file' 'interactionFiles/$identifier' &&
20 #end for
21
22 #if $differentialFiles:
23 #for $file in $differentialFiles:
24 #set identifier = @ESCAPE_IDENTIFIER_FILE@
25 ln -s '$file' 'differentialFolder/$identifier' &&
26 #end for
27 #end if
28
29 #if $significantFiles:
30 #for $file in $significantFiles:
31 #set identifier = @ESCAPE_IDENTIFIER_FILE@
32 ln -s '$file' 'significantFolder/$identifier' &&
33 #end for
34 #end if
35
36 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
37 #set $interactonfileslist = ' '.join([ '\'interactionFiles/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $interactionFiles ])
38 #set $differentialfileslist = ' '.join([ '\'differentialFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $differentialFiles ])
39 #set $significantfileslist = ' '.join([ '\'significantFolder/%s\'' % @ESCAPE_IDENTIFIER_FILE@ for $file in $significantFiles ])
40
41 #end if
42
43 @BINARY@
44 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
45 --interactionFile $interactonfileslist
46 #if $differentialFiles:
47 --differentialTestResult $differentialfileslist
48 #end if
49
50 #if $significantFiles:
51 --significantInteractions $significantfileslist
52 #end if
53
54 -o out_plot.$image_file_format
55 #else:
56 --interactionFile $batchmode_conditional.interactionFilesOrderFile
57 --interactionFileFolder interactionFiles
58 #if $batchmode_conditional.differentialFilesOrderFile:
59 --differentialTestResult $batchmode_conditional.differentialFilesOrderFile
60 --differentialTestResultsFolder differentialFolder
61 #end if
62 #if $batchmode_conditional.significantInteractionFilesOrderFile:
63 --significantInteractions $batchmode_conditional.significantInteractionFilesOrderFile
64 --significantInteractionFileFolder significantFolder
65 #end if
66 --plotSampleNumber $batchmode_conditional.computeSampleNumber
67
68 --batchMode
69 --outputFolder plots
70 --outputFormat $image_file_format
71
72
73 #end if
74
75 --range $rangeUpstream $rangeDownstream
76 #if $backgroundModelFile:
77 --backgroundModelFile $backgroundModelFile
78 #end if
79
80 #if $dpi:
81 --dpi $dpi
82 #end if
83
84 #if $maxPValue:
85 --maxPValue $maxPValue
86 #end if
87
88 #if $minPValue:
89 --minPValue $minPValue
90 #end if
91
92 --binResolution $resolution
93 #if $colormap:
94 --colorMapPvalue $colormap
95 #end if
96
97 $pvalue
98 #if $xFold:
99 --xFold $xFold
100 #end if
101 --colorList $colorList
102 --threads @THREADS@
103
104 #if $batchmode_conditional.batchmode_selector == 'optionSinglemode':
105 && mv out_plot.$image_file_format plots/out_plot.$image_file_format
106 #end if
107 ]]></command>
108 <inputs>
109 <param name='interactionFiles' type="data" format="interval" label="Interaction files" multiple="true"/>
110 <param name='differentialFiles' type="data" format="interval" label="Rejected H0 files" multiple="true" optional='true'/>
111 <param name='significantFiles' type="data" format="interval" label="Significant interaction files" multiple="true" optional='true'/>
112
113 <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.' />
114 <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.' />
115 <param argument="--backgroundModelFile" type="data" format='tabular'
116 label="Background model"
117 help="The background file computed by chicViewpointBackgroundModel" optional='true'/>
118
119 <conditional name="batchmode_conditional">
120 <param name="batchmode_selector" type="select" label="Compute files individually or in batch mode">
121 <option value="optionBatchmode">Batch processing</option>
122 <option value="optionSinglemode" selected="True">Single file processing</option>
123 </param>
124 <when value="optionBatchmode">
125 <param name='interactionFilesOrderFile' type="data" format="txt" label="Interaction file order"/>
126 <param name='differentialFilesOrderFile' type="data" format="txt" label="Rejected H0 file order" optional='true'/>
127 <param name='significantInteractionFilesOrderFile' type="data" format="txt" label="Significant file order" optional='true'/>
128 <param name='computeSampleNumber' type="integer" value='2' label="Plot n sample in one plot"/>
129
130 </when>
131 <when value="optionSinglemode">
132 </when>
133 </conditional>
134
135
136 <param argument="--maxPValue" type="float" optional="true" label="Max p-value" help="Maximum value of the plotted p-value."/>
137 <param argument="--minPValue" type="float" optional="true" label="Min p-value" help="Minimum value of the plotted p-value."/>
138 <param name='resolution' type='integer' value='1000' label='Resolution of cHi-C data' help='Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.' optional='true'/>
139 <param name='pvalue' type='boolean' truevalue='--pValue' falsevalue="" checked="false" label="Plot p-values as a colorbar"/>
140 <expand macro="colormap" />
141
142 <param name='xFold' type='float' value='' label='X-fold mean background' help='Plot x-fold region for the mean background.' optional='true'/>
143
144 <param name="image_file_format" type="select" label="Image output format">
145 <option value="png" selected="True">png</option>
146 <option value="svg">svg</option>
147 <option value="pdf">pdf</option>
148 </param>
149 <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
150 <param name='colorList' type='text' value='g b c m y k' label='Color list' help='Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/3.1.0/gallery/color/named_colors.html' optional='true'/>
151
152
153 </inputs>
154 <outputs>
155 <collection name="plotsCollection" type="list" label="cHi-C viewpoint plots">
156 <discover_datasets pattern="__name_and_ext__" directory="plots" />
157 </collection>
158
159 </outputs>
160 <tests>
161 <test>
162 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed,cHi-C/chicViewpoint/output_1/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed"/>
163 <param name="differentialFiles" value="cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_4487435_4487435_Sox17_H0_rejected.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_14300280_14300280_Eya1_H0_rejected.bed,cHi-C/chicDifferentialTest/batch_mode_fisher_outfile/FL-E13-5_MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_H0_rejected.bed"/>
164 <param name="significantFiles" value="cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_4487435_4487435_Sox17_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_14300280_14300280_Eya1_output_significant.bed,cHi-C/chicSignificantInteractions/output_5/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d_output_significant.bed"/>
165
166
167 <conditional name="batchmode_conditional">
168 <param name="batchmode_selector" value='optionBatchmode'/>
169 <param name="interactionFilesOrderFile" value='cHi-C/chicViewpoint/fileNames_two_matrices.txt'/>
170 <param name="differentialFilesOrderFile" value='cHi-C/chicDifferentialTest/rejectedFilesList.txt'/>
171 <param name="significantInteractionFilesOrderFile" value='cHi-C/chicSignificantInteractions/output_5_significant_files.txt'/>
172 <param name='computeSampleNumber' value='2'/>
173 </conditional>
174 <param name="pvalue" value='True'/>
175 <param name="alpha" value='0.5'/>
176 <param name='backgroundModelFile' value='cHi-C/background.bed'/>
177 <param name='xFold' value='1.5'/>
178 <output_collection name="plotsCollection" type="list" count="3">
179 <element name="Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280" file="cHi-C/chicPlotViewpoint/batchMode/two/Eya1_FL-E13-5_MB-E10-5_chr1_chr1_14300280.png" ftype="png" compare='sim_size' delta='40000'/>
180 <element name="Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435" file="cHi-C/chicPlotViewpoint/batchMode/two/Sox17_FL-E13-5_MB-E10-5_chr1_chr1_4487435.png" ftype="png" compare='sim_size' delta='40000'/>
181 <element name="Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103" file="cHi-C/chicPlotViewpoint/batchMode/two/Tfap2d_FL-E13-5_MB-E10-5_chr1_chr1_19093103.png" ftype="png" compare='sim_size' delta='40000'/>
182 </output_collection>
183
184 </test>
185 <test>
186 <param name="interactionFiles" value="cHi-C/chicViewpoint/output_1/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed"/>
187
188 <conditional name="batchmode_conditional">
189 <param name="batchmode_selector" value='optionSinglemode'/>
190 </conditional>
191
192 <output_collection name="plotsCollection" type="list" count="1">
193 <element name="out_plot" file="cHi-C/chicPlotViewpoint/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.png" ftype="png" compare='sim_size' delta='40000'/>
194
195 </output_collection>
196 </test>
197 </tests>
198 <help><![CDATA[
199
200 Plot of viewpoints
201 ==================
202
203 chicPlotViewpoint plots one or many viewpoints with the average background model and the computed p-value per sample. Moreover it can highlight differential interactions of two samples and or significant regions.
204
205 An example usage is:
206
207 `$ chicPlotViewpoint --interactionFile viewpoint1.bed viewpoint2.bed --range 500000 500000 --backgroundModelFile background_model.bed --pValue --outFileName viewpoint1_2.png --dpi 300`
208
209
210 In batch mode the list of file names and the folders containing the files need to be given:
211
212 `$ chicPlotViewpoint --interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder --differentialTestResult rejected_H0.txt --differentialTestResultsFolder differentialFolder --range 500000 500000 --backgroundModelFile background_model.bed --pValue --outputFolder plotsFOlder --dpi 300 --threads 20`
213
214
215 For more information about HiCExplorer please consider our documentation on readthedocs.io_
216
217 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
218 ]]></help>
219 <expand macro="citations" />
220 </tool>