Mercurial > repos > bgruening > hicexplorer_chicviewpoint

comparison chicViewpoint.xml @ 2:0dabfd9a496b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 4b602d427e0fc0da5353a4510798349de98e4ae4"
author iuc
date Wed, 11 Mar 2020 17:23:23 -0400
parents 68c92dfd03d7
children 8fb584526458
comparison
equal deleted inserted replaced
1:68c92dfd03d7 2:0dabfd9a496b
12 #for $m in $matrix_h5_cooler_multiple: 12 #for $m in $matrix_h5_cooler_multiple:
13 #set identifier = @ESCAPE_IDENTIFIER_M@ 13 #set identifier = @ESCAPE_IDENTIFIER_M@
14 ln -s '$m' '$identifier' && 14 ln -s '$m' '$identifier' &&
15 #end for 15 #end for
16 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ]) 16 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])
17 17
18 @BINARY@ 18 @BINARY@
19 19
20 --matrices $m 20 --matrices $m
21 --range $rangeUpstream $rangeDownstream 21 --range $rangeUpstream $rangeDownstream
22 --referencePoints '$referencePoints' 22 --referencePoints '$referencePoints'
33 33
34 <param argument="--referencePoints" type="data" format='interval' 34 <param argument="--referencePoints" type="data" format='interval'
35 label="Reference points" 35 label="Reference points"
36 help="Bed file contains all reference points which should be used to create viewpoints." /> 36 help="Bed file contains all reference points which should be used to create viewpoints." />
37 <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.' /> 37 <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.' />
38 <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.' /> 38 <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.' />
39 39
40 <param argument="--backgroundModelFile" type="data" format='tabular' 40 <param argument="--backgroundModelFile" type="data" format='tabular'
41 label="Background model" 41 label="Background model"
42 help="The background file computed by chicViewpointBackgroundModel" /> 42 help="The background file computed by chicViewpointBackgroundModel" />
43 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/> 43 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
44 <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.'/> 44 <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.'/>
45 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)" 45 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)"
46 help="Set this parameter if you want to use the batch processing mode for the further analysis."/> 46 help="Set this parameter if you want to use the batch processing mode for the further analysis."/>
47 </inputs> 47 </inputs>
48 <outputs> 48 <outputs>
49 <collection name="interactionFilesCollection" type="list" label="Interaction files"> 49 <collection name="interactionFilesCollection" type="list" label="Interaction files">
54 </data> 54 </data>
55 </outputs> 55 </outputs>
56 <tests> 56 <tests>
57 <test> 57 <test>
58 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 58 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
59 59
60 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/> 60 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
61 <param name="backgroundModelFile" value="cHi-C/background.bed"/> 61 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
62 <param name="fixateRange" value="500000"/> 62 <param name="fixateRange" value="500000"/>
63 <param name="rangeUpstream" value="200000"/> 63 <param name="rangeUpstream" value="200000"/>
64 <param name="rangeDownstream" value="200000"/> 64 <param name="rangeDownstream" value="200000"/>
65 <param name="writeFileNamesToFile" value="True"/> 65 <param name="writeFileNamesToFile" value="True"/>
66 66
67 67
68 <output_collection name="interactionFilesCollection" type="list" count="6"> 68 <output_collection name="interactionFilesCollection" type="list" count="6">
69 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/> 69 <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"/>
70 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/> 70 <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"/>
71 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/> 71 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
72 72
73 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/> 73 <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"/>
74 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/> 74 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
75 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/> 75 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
76 </output_collection> 76 </output_collection>
77 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> 77 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/>
78 78
79 </test> 79 </test>
80 <test> 80 <test>
81 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/> 81 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
82 82
83 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/> 83 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
84 <param name="backgroundModelFile" value="cHi-C/background.bed"/> 84 <param name="backgroundModelFile" value="cHi-C/background.txt"/>
85 <param name="fixateRange" value="500000"/> 85 <param name="fixateRange" value="500000"/>
86 <param name="rangeUpstream" value="200000"/> 86 <param name="rangeUpstream" value="200000"/>
87 <param name="rangeDownstream" value="200000"/> 87 <param name="rangeDownstream" value="200000"/>
88 <param name="writeFileNamesToFile" value="False"/> 88 <param name="writeFileNamesToFile" value="False"/>
89 89
90 90
91 <output_collection name="interactionFilesCollection" type="list" count="6"> 91 <output_collection name="interactionFilesCollection" type="list" count="6">
92 <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/> 92 <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"/>
93 <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/> 93 <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"/>
94 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/> 94 <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.txt" ftype="interval" lines_diff="3"/>
95 95
96 <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/> 96 <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"/>
97 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/> 97 <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.txt" ftype="interval" lines_diff="3"/>
98 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/> 98 <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.txt" ftype="interval" lines_diff="3"/>
99 </output_collection> 99 </output_collection>
100 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> --> 100 <!-- <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/> -->
101 101
102 </test> 102 </test>
103 </tests> 103 </tests>
104 <help><![CDATA[ 104 <help><![CDATA[
105 105
106 Compute viewpoints for all given reference points 106 Compute viewpoints for all given reference points
107 ================================================= 107 =================================================
108 108
109 Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, the files 109 Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, the files
110 are named by the name of the reference point, the sample name and the location of the reference point: 110 are named by the name of the reference point, the sample name and the location of the reference point:
111 111
112 gene_matrix_name_chr_start_end.bed 112 gene_matrix_name_chr_start_end.txt
113 113
114 If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this 114 If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this
115 file all the file names will be written to; in the case of multiple samples two consecutive lines are consideres as treatment vs control in the differential analysis. 115 file, all the file names will be written to; in the case of multiple samples two consecutive lines are considered as treatment vs control in the differential analysis.
116 116
117 For more information about HiCExplorer please consider our documentation on readthedocs.io_ 117 For more information about HiCExplorer please consider our documentation on readthedocs.io_
118 118
119 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 119 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
120 ]]></help> 120 ]]></help>