Mercurial > repos > bgruening > hicexplorer_hichyperoptdetectloops

comparison hicHyperoptDetectLoops.xml @ 0:dde6b320a34b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 55de003830db380639df997cdc5810df8022f63e"
author bgruening
date Tue, 16 Mar 2021 20:14:14 +0000
parents
children 7f7c6ead2d0d
comparison
equal deleted inserted replaced
-1:000000000000 0:dde6b320a34b
1 <tool id="hicexplorer_hichyperoptDetectLoops" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>optimizes parameters for hicDetectLoops</description>
3 <macros>
4 <token name="@BINARY@">hicHyperoptDetectLoops</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
10 @BINARY@
11
12 --matrix 'matrix.$matrix_h5_cooler.ext'
13
14 #if '$proteinFile':
15 --proteinFile '$proteinFile'
16 #end if
17
18 #if '$maximumNumberOfLoops':
19 --maximumNumberOfLoops '$maximumNumberOfLoops'
20 #end if
21
22 #if '$resolution':
23 --resolution '$resolution'
24 #end if
25
26 #if '$runs':
27 --runs '$runs'
28 #end if
29
30 --outputFileName hyperopt_result.txt
31
32 --threads @THREADS@
33 ]]>
34 </command>
35 <inputs>
36 <expand macro="matrix_h5_cooler_macro" />
37 <param argument="--proteinFile" type='data' format="bed" label="Protein peak file in bed format" help= "The protein file to validate the detected loops." />
38 <param argument="--maximumNumberOfLoops" type="integer" min='0' max='100000' label="Maximum number of loops" help= "The maximum number of loops that should be used for optimization computation." value='10000' />
39 <param argument="--resolution" type="integer" min='0' max='100000000' label="Resolution of the matrix" help="The matrix resolution of the Hi-C interaction matrix." value='10000' />
40 <param argument="--runs" type="integer" min='2' max='10000' label="Hyperopt runs" help= "The number of iterations hyperopt uses to search for a result" value='100' />
41 </inputs>
42 <outputs>
43 <data name='hyperopt_result' from_work_dir='hyperopt_result.txt' format='txt' label='Computed parameters for hicDetectLoops' />
44 </outputs>
45 <tests>
46 <test>
47 <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
48 <param name="proteinFile" value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak" />
49 <param name="maximumNumberOfLoops" value="5" />
50 <param name="resolution" value="2" />
51 <param name="runs" value="5" />
52 <output name="hyperopt_result" file="hicHyperoptDetectLoops/loops.bedgraph" ftype="txt" compare="sim_size" />
53 </test>
54 </tests>
55 <help><![CDATA[
56
57 Hyperopt parameter optimization loop detection
58 ==============================================
59
60 Compute with a protein peak data file (bed format) optimal parameters for the loop calling. Useful proteins are e.g. CTCF or cohesin.
61
62 _________________
63
64 Usage
65 -----
66
67 A command line example is available below (easily matchable in Galaxy using each field information):
68
69 ̀`$ hicHyperoptDetectLoops -m matrix.cool -o hyperopt_result.txt --maximumNumberOfLoops 10000 --resolution 10000 --runs 100`
70
71
72 For more information about HiCExplorer please consider our documentation on readthedocs.io_.
73
74 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
75
76 ]]> </help>
77 <expand macro="citations" />
78 </tool>