Mercurial > repos > iuc > pretext_map

annotate pretext_map.xml @ 0:7c2e9bc2123b 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/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
author iuc
date Wed, 05 May 2021 15:09:54 +0000
parents
children 02831bf9e95f
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0
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
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1 <tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
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2 <macros>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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3 <token name="@TOOL_VERSION@">0.1.5</token>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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4 <token name="@VERSION_SUFFIX@">0</token>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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5 </macros>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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6 <requirements>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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7 <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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8 <requirement type="package" version="1.12">samtools</requirement>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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9 </requirements>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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10 <version_command>PretextMap --version</version_command>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
iuc
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11 <command detect_errors="exit_code"><![CDATA[
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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12 #if $input.is_of_type("bam"):
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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13 samtools view -h '${input}' |
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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14 #else
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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15 cat '${input}' |
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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16 #end if
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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17 PretextMap
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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18 #if $sorting.sortby == "length":
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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19 --sortby length
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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20 --sortorder $sorting.sortorder
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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21 #elif $sorting.sortby == "name":
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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22 --sortby name
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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23 --sortorder $sorting.sortorder
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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24 #end if
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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25 #if $map_qual:
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26 --mapq $map_qual
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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27 #end if
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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28 #if $filter.filter_type == "in":
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29 --filterInclude '$filter.filter_list'
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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30 #elif $filter.filter_type == "out":
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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31 --filterExclude '$filter.filter_list'
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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32 #end if
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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33 -o output.pretext
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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34 ]]></command>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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35 <inputs>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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36 <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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37 <conditional name="sorting">
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38 <param argument="--sortby" type="select" label="Sort by">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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39 <option value="nosort" selected="true">Don't sort</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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40 <option value="length">Length</option>
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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41 <option value="name">Name</option>
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42 </param>
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43 <when value="nosort"/>
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44 <when value="length">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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45 <param argument="--sortorder" type="select" label="Sort order: ">
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46 <option value="ascend">Ascending</option>
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47 <option value="decend">Decending</option>
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48 </param>
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49 </when>
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50 <when value="name">
7c2e9bc2123b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit f2ac7d9fe461223fe026dba40837333d0813c679"
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51 <param argument="--sortorder" type="select" label="Sort order: ">
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52 <option value="ascend">Ascending</option>
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53 <option value="descend">Decending</option>
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54 </param>
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55 </when>
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56 </conditional>
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57 <param name="map_qual" type="integer" label="Minimum mapping quality:" min="0" optional="true"/>
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58 <conditional name="filter">
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59 <param name="filter_type" type="select" label="How to filter: ">
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60 <option value="" selected="true">No filter</option>
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61 <option value="in">Filter to include only specified sequence names</option>
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62 <option value="out">Filter to exclude specified sequence names</option>
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63 </param>
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64 <when value=""/>
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65 <when value="in">
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66 <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
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67 <sanitizer>
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68 <valid initial="string.ascii_letters,string.digits">
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69 <add value="_"/>
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70 </valid>
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71 </sanitizer>
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72 </param>
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73 </when>
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74 <when value="out">
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75 <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1, seq_2">
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76 <sanitizer>
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77 <valid initial="string.ascii_letters,string.digits">
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78 <add value="_"/>
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79 </valid>
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80 </sanitizer>
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81 </param>
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82 </when>
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83 </conditional>
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84 </inputs>
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85 <outputs>
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86 <data format="pretext" name="pretext_map_out" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
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87 </outputs>
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88 <tests>
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89 <test>
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90 <param name="input" ftype="bam" value="test.bam"/>
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91 <conditional name="sorting">
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92 <param name="sortby" value="length"/>
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93 <param name="sortorder" value="ascend"/>
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94 </conditional>
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95 <conditional name="filter">
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96 <param name="filter_type" value="in"/>
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97 <param name="filter_list" value="ref"/>
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98 </conditional>
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99 <param name="map_qual" value="10"/>
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100 <output name="pretext_map_out" file="output_1.pretext"/>
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101 </test>
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102 <test>
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103 <param name="input" ftype="sam" value="test.sam"/>
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104 <conditional name="sorting">
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105 <param name="sortby" value="name"/>
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106 <param name="sortorder" value="descend"/>
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107 </conditional>
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108 <conditional name="filter">
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109 <param name="filter_type" value="out"/>
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110 <param name="filter_list" value="chrM, chr8, chr9"/>
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111 </conditional>
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112 <output name="pretext_map_out" file="output_2.pretext"/>
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113 </test>
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114 </tests>
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115 <help><![CDATA[
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116
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117 **What is does**
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118
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119 The Paired REad TEXTure Mapper converts aligned read pairs into genome contact maps.
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120 Pretext has no special requirement on the alignment files
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121 process your alignments however you want before feeding to PretextMap.
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122
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123 ]]></help>
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124 <citations>
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125 <citation type="bibtex">
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126 @misc{Harry_et_al,
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127 Author={Harry, E},
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128 title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},
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129 url = {https://github.com/wtsi-hpag/PretextSnapshot},}
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130 </citation>
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131 </citations>
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132 </tool>