Mercurial > repos > bgruening > hicexplorer_chicviewpoint

comparison chicViewpoint.xml @ 8:f881c94fb3b3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
author iuc
date Wed, 18 Oct 2023 10:44:35 +0000
parents dbfd2cfc0f66
children
comparison
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7:fdcf45efac66 8:f881c94fb3b3
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #import re 9 #import re
10 10
11 mkdir interactionFiles &&
12 #for $m in $matrix_h5_cooler_multiple: 11 #for $m in $matrix_h5_cooler_multiple:
13 #set identifier = @ESCAPE_IDENTIFIER_M@ 12 #set identifier = @ESCAPE_IDENTIFIER_M@
14 ln -s '$m' '$identifier' && 13 ln -s '$m' '$identifier' &&
15 #end for 14 #end for
16 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ]) 15 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])
19 --matrices $m 18 --matrices $m
20 --range $rangeUpstream $rangeDownstream 19 --range $rangeUpstream $rangeDownstream
21 --referencePoints '$referencePoints' 20 --referencePoints '$referencePoints'
22 --averageContactBin $averageContactBin 21 --averageContactBin $averageContactBin
23 --fixateRange $fixateRange 22 --fixateRange $fixateRange
24 --decimalPlaces $decimalPlaces
25 --threads @THREADS@ 23 --threads @THREADS@
26 --backgroundModelFile '$backgroundModelFile' 24 --backgroundModelFile '$backgroundModelFile'
27 --outputFolder interactionFiles 25 --outFileName interactionFiles.hdf5
28 $writeFileNamesToFile
29
30 #if $tar:
31 && cd interactionFiles
32 && tar -cvf ../viewpoints.tar .
33 && cd ..
34 && rm -rf interactionFiles
35 #end if
36 26
37 ]]> </command> 27 ]]> </command>
38 <inputs> 28 <inputs>
39 <expand macro="matrix_h5_cooler_multiple_macro" /> 29 <expand macro="matrix_h5_cooler_multiple_macro" />
40 30
41 <param argument="--referencePoints" type="data" format='interval' label="Reference points" help="Bed file contains all reference points which should be used to create viewpoints." /> 31 <param argument="--referencePoints" type="data" format="interval" label="Reference points" help="Bed file contains all reference points which should be used to create viewpoints." />
42 <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.' /> 32 <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." />
43 <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.' /> 33 <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." />
44 34
45 <param argument="--backgroundModelFile" type="data" format='tabular' label="Background model" help="The background file computed by chicViewpointBackgroundModel" /> 35 <param argument="--backgroundModelFile" type="data" format="tabular" label="Background model" help="The background file computed by chicViewpointBackgroundModel" />
46 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.' /> 36 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help="Average the contacts of n bins via a sliding window approach." />
47 <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.' /> 37 <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." />
48 <param argument="--decimalPlaces" type="integer" value="12" label="Decimal places for output" help='Decimal places for all floating value in the output.' />
49
50 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" help="Set this parameter if you want to use the batch processing mode for the further analysis." />
51 <param name='tar' type='boolean' checked="false" label="tar output to one file" help="The output is tarred to one file and not written to a collection. Set this option if the number of files is large." />
52
53 </inputs> 38 </inputs>
54 <outputs> 39 <outputs>
55 <collection name="interactionFilesCollection" type="list" label="Interaction files"> 40 <data name="interactionFileNames" from_work_dir="interactionFiles.hdf5" format="h5" label="${tool.name} interaction file" />
56 <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" />
57 </collection>
58 <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names">
59 <filter>writeFileNamesToFile</filter>
60 </data>
61 <data name="interactionFilesTar" from_work_dir="viewpoints.tar" format="tar" label="${tool.name} interaction file names tar">
62 <filter>tar</filter>
63 </data>
64 </outputs> 41 </outputs>
65 <tests> 42 <tests>
66 <test> 43 <test>
67 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" /> 44 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
68 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" /> 45 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
69 <param name="backgroundModelFile" value="cHi-C/background.txt" /> 46 <param name="backgroundModelFile" value="cHi-C/background.txt" />
70 <param name="fixateRange" value="500000" /> 47 <param name="fixateRange" value="500000" />
71 <param name="rangeUpstream" value="200000" /> 48 <param name="rangeUpstream" value="200000" />
72 <param name="rangeDownstream" value="200000" /> 49 <param name="rangeDownstream" value="200000" />
73 <param name="writeFileNamesToFile" value="True" /> 50 <output name="interactionFileNames" ftype="h5">
74 51 <assert_contents>
75 <output_collection name="interactionFilesCollection" type="list" count="6"> 52 <has_h5_attribute key="averageContactBin" value="5" />
76 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3" /> 53 <has_h5_attribute key="fixateRange" value="500000" />
77 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3" /> 54 <!-- <has_h5_attribute key="range" value="200000,200000" /> -->
78 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval"> 55 <has_h5_attribute key="resolution" value="1000" />
79 <assert_contents> 56 <has_h5_attribute key="type" value="interactions" />
80 <has_text text="18895000" /> 57 </assert_contents>
81 <has_text text="chr1" /> 58 </output>
82 <has_text text="Tfap2d" />
83 <has_text text="interactions" />
84 <has_text text="472.0" />
85 </assert_contents>
86 </element>
87 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3" />
88 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval">
89 <assert_contents>
90 <has_text text="14100000" />
91 <has_text text="chr1" />
92 <has_text text="Eya1" />
93 <has_text text="interactions" />
94 <has_text text="832.0" />
95 </assert_contents>
96 </element>
97 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval">
98 <assert_contents>
99 <has_text text="4455000" />
100 <has_text text="chr1" />
101 <has_text text="Sox17" />
102 <has_text text="interactions" />
103 <has_text text="978.0" />
104 <has_text text="-30000" />
105 </assert_contents>
106 </element>
107 </output_collection>
108 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' />
109 </test>
110 <test>
111 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
112 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
113 <param name="backgroundModelFile" value="cHi-C/background.txt" />
114 <param name="fixateRange" value="500000" />
115 <param name="rangeUpstream" value="200000" />
116 <param name="rangeDownstream" value="200000" />
117 <param name="writeFileNamesToFile" value="False" />
118 <output_collection name="interactionFilesCollection" type="list" count="6">
119 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3" />
120 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3" />
121 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval">
122 <assert_contents>
123 <has_text text="18893000" />
124 <has_text text="chr1" />
125 <has_text text="Tfap2d" />
126 <has_text text="interactions" />
127 <has_text text="472.0" />
128 </assert_contents>
129 </element>
130 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3" />
131 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval">
132 <assert_contents>
133 <has_text text="14103000" />
134 <has_text text="chr1" />
135 <has_text text="Eya1" />
136 <has_text text="interactions" />
137 <has_text text="832.0" />
138 <has_text text="-199000" />
139 </assert_contents>
140 </element>
141 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval">
142 <assert_contents>
143 <has_text text="4455000" />
144 <has_text text="chr1" />
145 <has_text text="Sox17" />
146 <has_text text="interactions" />
147 <has_text text="978.0" />
148 <has_text text="-30000" />
149 </assert_contents>
150 </element>
151 </output_collection>
152 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> -->
153 </test>
154 <test>
155 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool" />
156 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed" />
157 <param name="backgroundModelFile" value="cHi-C/background.txt" />
158 <param name="fixateRange" value="500000" />
159 <param name="rangeUpstream" value="200000" />
160 <param name="rangeDownstream" value="200000" />
161 <param name="writeFileNamesToFile" value="True" />
162 <param name='tar' value='True' />
163 <output name="interactionFilesTar" file="cHi-C/chicViewpoint/viewpoints.tar" ftype='tar' compare="sim_size" delta='40000' />
164 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0' />
165 </test> 59 </test>
166 </tests> 60 </tests>
167 <help><![CDATA[ 61 <help><![CDATA[
168 62
169 Compute viewpoints for all given reference points 63 Compute viewpoints for all given reference points