Mercurial > repos > bgruening > hicexplorer_hicinfo
comparison hicInfo.xml @ 0:708e1b8eff5c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"
author | bgruening |
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date | Mon, 16 Dec 2019 14:34:49 -0500 |
parents | |
children | ca97d2b2b59e |
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-1:000000000000 | 0:708e1b8eff5c |
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1 <tool id="hicexplorer_hicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0"> | |
2 <description>transform a matrix to obs/exp, pearson and covariance matrices</description> | |
3 <macros> | |
4 <token name="@BINARY@">hicInfo</token> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command detect_errors="exit_code"><![CDATA[ | |
9 | |
10 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' && | |
11 @BINARY@ --matrices 'matrix_name.$matrix_h5_cooler.ext' | |
12 -o hicInfo.txt | |
13 ]]> | |
14 </command> | |
15 <inputs> | |
16 <expand macro='matrix_h5_cooler_macro' /> | |
17 </inputs> | |
18 <outputs> | |
19 <data name="info" from_work_dir="hicInfo.txt" format="txt" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: matrix info"/> | |
20 </outputs> | |
21 <tests> | |
22 <test> | |
23 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/> | |
24 <output name="info" file="hicInfo/hicInfo_output.txt" ftype="txt" lines_diff="3"/> | |
25 </test> | |
26 </tests> | |
27 <help><![CDATA[ | |
28 | |
29 Get information about you Hi-C matrix | |
30 ===================================== | |
31 | |
32 This scripts returns useful information about your Hi-C interaction matrix. However, the following information can be included if it is provided by the Hi-C interaction matrix meta data. In case the meta data is missing, the information can be less. | |
33 | |
34 .. code-block:: text | |
35 | |
36 # Matrix information file. Created with HiCExplorer's hicInfo version 3.2-dev | |
37 File: /tmp/tmpyyll1kwi.cool | |
38 Date: 2019-08-11T19:46:15.959678 | |
39 Genome assembly: dm3 | |
40 Size: 33,754 | |
41 Bin_length: 5000 | |
42 Number of chromosomes: 15 | |
43 Non-zero elements: 35,857 | |
44 The following columns are available: ['chrom' 'start' 'end'] | |
45 | |
46 | |
47 Generated by: HiCMatrix-11-dev | |
48 Cooler library version: cooler-0.8.5 | |
49 HiCMatrix url: https://github.com/deeptools/HiCMatrix | |
50 Interaction matrix created with: HiCExplorer-3.2-dev | |
51 URL: https://github.com/deeptools/HiCExplorer | |
52 | |
53 | |
54 Build statistics: | |
55 | |
56 File /tmp/tmpyyll1kwi.cool | |
57 Sequenced reads 99983 | |
58 Min rest. site distance 300 | |
59 Max library insert size 1000 | |
60 | |
61 # count (percentage w.r.t. total sequenced reads) | |
62 Pairs mappable, unique and high quality 52726 (52.73) | |
63 Hi-C contacts 37321 (37.33) | |
64 One mate unmapped 8777 (8.78) | |
65 One mate not unique 3603 (3.60) | |
66 Low mapping quality 34877 (34.88) | |
67 | |
68 # count (percentage w.r.t. mappable, unique and high quality pairs) | |
69 dangling end 0 (0.00) | |
70 self ligation (removed) 0 (0.00) | |
71 One mate not close to rest site 0 (0.00) | |
72 same fragment 15393 (29.19) | |
73 self circle 0 (0.00) | |
74 duplicated pairs 12 (0.02) | |
75 | |
76 # count (percentage w.r.t. total valid pairs used) | |
77 inter chromosomal 5955 (15.96) | |
78 Intra short range (< 20kb) 8853 (23.72) | |
79 Intra long range (>= 20kb) 22513 (60.32) | |
80 Read pair type: inward pairs 7145 (19.14) | |
81 Read pair type: outward pairs 9731 (26.07) | |
82 Read pair type: left pairs 7156 (19.17) | |
83 Read pair type: right pairs 7334 (19.65) | |
84 | |
85 | |
86 Please have in mind that the provided information depends on the tool and its version with which the matrix was created. | |
87 | |
88 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ | |
89 | |
90 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html | |
91 ]]></help> | |
92 <expand macro="citations" /> | |
93 </tool> |