Mercurial > repos > bgruening > hicexplorer_chicviewpointbackgroundmodel

comparison chicViewpointBackgroundModel.xml @ 0:bd11c6a972ef 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 15:32:01 -0500
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children 91abc3b2e948
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-1:000000000000 0:bd11c6a972ef
1 <tool id="hicexplorer_chicviewpointbackgroundmodel" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>validate detected loops with protein peaks.</description>
3 <macros>
4 <token name="@BINARY@">chicViewpointBackgroundModel</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
11 ln -s '$m' '${counter}_matrix.$m.ext' &&
12 #end for
13 #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
14
15 @BINARY@
16
17 --matrices $m
18 --averageContactBin $averageContactBin
19 --fixateRange $fixateRange
20 --referencePoints '$referencePoints'
21 --threads @THREADS@
22 --outFileName background.txt
23 ]]></command>
24 <inputs>
25 <expand macro="matrix_h5_cooler_multiple_macro" />
26
27 <param argument="--referencePoints" type="data" format='interval'
28 label="Reference points"
29 help="Bed file contains all reference points which should be used to build the background model." />
30 <param argument="--averageContactBin" type="integer" value="5" label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>
31 <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.'/>
32
33 </inputs>
34 <outputs>
35 <data name="background" from_work_dir="background.txt" format="tabular" label="${tool.name} on [${on_string}]: Background model"/>
36 </outputs>
37 <tests>
38 <test>
39 <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
40
41 <param name="referencePoints" value="cHi-C/referencePoints.bed"/>
42
43 <output name="background" file="cHi-C/background.bed" ftype="tabular" compare="sim_size" delta='40000'/>
44 </test>
45 </tests>
46 <help><![CDATA[
47
48 Compute a background model for cHi-C data analysis
49 ==================================================
50
51 chicViewpointBackgroundModel computes for all given samples with all reference points a background model. For all relative distances to a reference point
52 a negative binomial distribution is fitted. Moreover, for each relative distance to a reference point the average value for this location is computed. Both
53 background models are used, the first one for p-value and significance computation, the second one to filter out interactions with a less x-fold over mean.
54
55 The background distributions are fixed at `--fixateRange` i.e. all distances lower / higher than this value use the fixed background distribution.
56
57 For more information about HiCExplorer please consider our documentation on readthedocs.io_
58
59 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
60 ]]></help>
61 <expand macro="citations" />
62 </tool>