Mercurial > repos > bgruening > hicexplorer_hicinfo

annotate hicInfo.xml @ 1:0ce6274769cd 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 09:19:06 +0000
parents b87fd2fb52f4
children 47d192a19232
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b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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1 <tool id="hicexplorer_hicinfo" name="@BINARY@" version="@WRAPPER_VERSION@.0">
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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2 <description>get information about the content of a Hi-C matrix</description>
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3 <macros>
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4 <token name="@BINARY@">hicInfo</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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10 ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
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11 @BINARY@ --matrices 'matrix_name.$matrix_h5_cooler.ext'
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12 -o hicInfo.txt
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13 ]]>
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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14 </command>
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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15 <inputs>
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16 <expand macro='matrix_h5_cooler_macro' />
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17 </inputs>
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18 <outputs>
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19 <data name="info" from_work_dir="hicInfo.txt" format="txt" label="${tool.name} on ${matrix_h5_cooler.name} [${on_string}]: matrix info"/>
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20 </outputs>
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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21 <tests>
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22 <test>
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23 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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24 <output name="info" file="hicInfo/hicInfo_output.txt" ftype="txt" lines_diff="3"/>
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25 </test>
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26 </tests>
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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27 <help><![CDATA[
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28
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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29 Get information about you Hi-C matrix
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30 =====================================
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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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.
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34 .. code-block:: text
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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35
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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36 # Matrix information file. Created with HiCExplorer's hicInfo version 3.2-dev
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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37 File: /tmp/tmpyyll1kwi.cool
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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38 Date: 2019-08-11T19:46:15.959678
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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39 Genome assembly: dm3
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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40 Size: 33,754
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41 Bin_length: 5000
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42 Number of chromosomes: 15
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43 Non-zero elements: 35,857
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44 The following columns are available: ['chrom' 'start' 'end']
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45
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46
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47 Generated by: HiCMatrix-11-dev
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48 Cooler library version: cooler-0.8.5
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49 HiCMatrix url: https://github.com/deeptools/HiCMatrix
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50 Interaction matrix created with: HiCExplorer-3.2-dev
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51 URL: https://github.com/deeptools/HiCExplorer
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52
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53
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54 Build statistics:
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55
1
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iuc
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56 File /tmp/tmpyyll1kwi.cool
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57 Sequenced reads 99983
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58 Min rest. site distance 300
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59 Max library insert size 1000
0
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60
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61 # count (percentage w.r.t. total sequenced reads)
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62 Pairs mappable, unique and high quality 52726 (52.73)
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63 Hi-C contacts 37321 (37.33)
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64 One mate unmapped 8777 (8.78)
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65 One mate not unique 3603 (3.60)
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66 Low mapping quality 34877 (34.88)
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67
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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68 # count (percentage w.r.t. mappable, unique and high quality pairs)
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69 dangling end 0 (0.00)
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70 self ligation (removed) 0 (0.00)
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71 One mate not close to rest site 0 (0.00)
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72 same fragment 15393 (29.19)
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73 self circle 0 (0.00)
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74 duplicated pairs 12 (0.02)
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75
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76 # count (percentage w.r.t. total valid pairs used)
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77 inter chromosomal 5955 (15.96)
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78 Intra short range (< 20kb) 8853 (23.72)
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79 Intra long range (>= 20kb) 22513 (60.32)
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80 Read pair type: inward pairs 7145 (19.14)
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81 Read pair type: outward pairs 9731 (26.07)
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82 Read pair type: left pairs 7156 (19.17)
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83 Read pair type: right pairs 7334 (19.65)
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84
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85
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86 Please have in mind that the provided information depends on the tool and its version with which the matrix was created.
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87
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88 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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90 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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91 ]]></help>
b87fd2fb52f4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 5744259254d4254a29cb7a6687fbbfd103301064"
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92 <expand macro="citations" />
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93 </tool>