Mercurial > repos > bgruening > hicexplorer_chicviewpoint

comparison chicViewpoint.xml @ 0:6d76e532b669 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 14:28:22 -0500
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children 68c92dfd03d7
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-1:000000000000 0:6d76e532b669
1 <tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>computes viewpoints with the given reference points and a background model.</description>
3 <macros>
4 <token name="@BINARY@">chicViewpoint</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 #for $m in $matrix_h5_cooler_multiple:
13 #set identifier = @ESCAPE_IDENTIFIER_M@
14 ln -s '$m' '$identifier' &&
15 #end for
16 #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])
17
18 @BINARY@
19
20 --matrices $m
21 --range $rangeUpstream $rangeDownstream
22 --referencePoints '$referencePoints'
23 --averageContactBin $averageContactBin
24 --fixateRange $fixateRange
25 --threads @THREADS@
26 --backgroundModelFile '$backgroundModelFile'
27 --outputFolder interactionFiles
28 $writeFileNamesToFile
29
30 ]]></command>
31 <inputs>
32 <expand macro="matrix_h5_cooler_multiple_macro" />
33
34 <param argument="--referencePoints" type="data" format='interval'
35 label="Reference points"
36 help="Bed file contains all reference points which should be used to create viewpoints." />
37 <param name="rangeUpstream" type="integer" value="500000" label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
38 <param name="rangeDownstream" type="integer" value="500000" label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
39
40 <param argument="--backgroundModelFile" type="data" format='tabular'
41 label="Background model"
42 help="The background file computed by chicViewpointBackgroundModel" />
43 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
44 <param argument="--fixateRange" type="integer" value="500000" label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>
45 <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt' falsevalue="" checked="false" label="Save interaction file names (batch processing)"
46 help="Set this parameter if you want to use the batch processing mode for the further analysis."/>
47 </inputs>
48 <outputs>
49 <collection name="interactionFilesCollection" type="list" label="Interaction files">
50 <discover_datasets pattern="__name__" format="interval" directory="interactionFiles" />
51 </collection>
52 <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names">
53 <filter>writeFileNamesToFile</filter>
54 </data>
55 </outputs>
56 <tests>
57 <test>
58 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
59
60 <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
61 <param name="backgroundModelFile" value="cHi-C/background.bed"/>
62 <param name="fixateRange" value="500000"/>
63 <param name="rangeUpstream" value="200000"/>
64 <param name="rangeDownstream" value="200000"/>
65 <param name="writeFileNamesToFile" value="True"/>
66
67
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"/>
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"/>
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"/>
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"/>
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"/>
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"/>
76 </output_collection>
77 <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/>
78
79 </test>
80 </tests>
81 <help><![CDATA[
82
83 Compute viewpoints for all given reference points
84 =================================================
85
86 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
87 are named by the name of the reference point, the sample name and the location of the reference point:
88
89 gene_matrix_name_chr_start_end.bed
90
91 If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this
92 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.
93
94 For more information about HiCExplorer please consider our documentation on readthedocs.io_
95
96 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
97 ]]></help>
98 <expand macro="citations" />
99 </tool>