Mercurial > repos > michal_klinka > trtools

annotate CompareSTR/compareSTR.xml @ 0:ecf8c4f9f8ba draft

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"planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
author michal_klinka
date Sat, 23 Apr 2022 16:34:03 +0000
parents
children 8e8cf43f6836
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ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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1 <?xml version="1.0" ?>
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2 <tool id="compareSTR" name="CompareSTR" version="@tool_version@">
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3 <description>CompareSTR compares different TR callsets generated on the same samples against the same reference
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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4 panel. CompareSTR outputs overall, per-locus, and per-sample concordance information.
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5 </description>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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10 <expand macro="requirements"/>
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11 <version_command>compareSTR --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 @INDEX_VCFS@
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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14 #set $old_names = [$str($required_arguments.vcf1), $str($required_arguments.vcf2)]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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15 #set $new_names = $get_new_vcf_names($old_names)
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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16 $index_vcfs($old_names, $new_names)
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17
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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18 compareSTR
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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19
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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20 ## end h definition
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21 ## vcf1 definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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22 #if $required_arguments.vcf1:
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23 --vcf1 $new_names[0]
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24 #end if
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25 ## end vcf1 definition
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26 ## vcf2 definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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27 #if $required_arguments.vcf2:
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28 --vcf2 $new_names[1]
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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29 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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30 ## end vcf2 definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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31 ## out definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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32 #if $required_arguments.out:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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33 --out $required_arguments.out
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34 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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35 ## end out definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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36 ## samples definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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37 #if $filtering_options.samples:
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38 --samples $filtering_options.samples
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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39 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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40 ## end samples definition
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41 ## region definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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42 #if $filtering_options.region:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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43 --region $filtering_options.region
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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44 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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45 ## end region definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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46 ## stratify_fields definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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47 #if $metrics_to_stratify_results.stratify_fields:
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48 --stratify-fields $metrics_to_stratify_results.stratify_fields
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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49 #end if
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50 ## end stratify_fields definition
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51 ## stratify_binsizes definition
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52 #if $metrics_to_stratify_results.stratify_binsizes:
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53 --stratify-binsizes $metrics_to_stratify_results.stratify_binsizes
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54 #end if
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55 ## end stratify_binsizes definition
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56 ## stratify_file definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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57 #if $metrics_to_stratify_results.stratify_file:
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58 --stratify-file $metrics_to_stratify_results.stratify_file
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59 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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60 ## end stratify_file definition
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61 ## period definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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62 #if $metrics_to_stratify_results.period:
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63 --period
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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64 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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65 ## end period definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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66 ## bubble_min definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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67 #if $plotting_options.bubble_min:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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68 --bubble-min $plotting_options.bubble_min
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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69 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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70 ## end bubble_min definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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71 ## bubble_max definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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72 #if $plotting_options.bubble_max:
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73 --bubble-max $plotting_options.bubble_max
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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74 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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75 ## end bubble_max definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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76 ## verbose definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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77 #if $optional_arguments.verbose:
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78 --verbose
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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79 #end if
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80 ## end verbose definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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81 ## numrecords definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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82 #if $optional_arguments.numrecords:
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83 --numrecords $optional_arguments.numrecords
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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84 #end if
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85 ## end numrecords definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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86 ## noplot definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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87 #if $optional_arguments.noplot:
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88 --noplot
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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89 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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90 ## end noplot definition
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91 ## vcftype1 definition
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92 #if $optional_arguments.vcftype1:
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93 --vcftype1 $optional_arguments.vcftype1
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94 #end if
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95 ## end vcftype1 definition
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96 ## vcftype2 definition
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97 #if $optional_arguments.vcftype2:
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98 --vcftype2 $optional_arguments.vcftype2
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99 #end if
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100 ## end vcftype2 definition
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101 ## ignore_phasing definition
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102 #if $optional_arguments.ignore_phasing:
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103 --ignore-phasing
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104 #end if
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105 ## end ignore_phasing definition
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106 ## version definition
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107 #if $versiondc8f.version:
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108 --version
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109 #end if
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110 ## end version definition
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111 1>$stdout 2>$stderr
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112 ]]></command>
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113
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114
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115 <inputs>
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116 <section name="required_arguments" title="Required arguments" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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117 <param argument="--vcf1" type="data" format="vcf_bgzip" optional="false" label="vcf1"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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118 help="First VCF file to compare (must be sorted, bgzipped, and indexed)"/>
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119 <param argument="--vcf2" type="data" format="vcf_bgzip" optional="false" label="vcf2"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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120 help="Second VCF file to compare (must be sorted, bgzipped, and indexed)"/>
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121 <param argument="--out" type="text" optional="false" label="out" help="Prefix to name output files"/>
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122 </section>
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123 <section name="filtering_options" title="Filtering options" expanded="false">
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124 <param argument="--samples" type="text" optional="true" label="samples"
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125 help="File containing list of samples to include"/>
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126 <param argument="--region" type="text" optional="true" label="region"
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127 help="Restrict to this region chrom:start-end"/>
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128 </section>
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129 <section name="metrics_to_stratify_results" title="Metrics to stratify results" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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130 <param argument="--stratify-fields" type="text" optional="true" label="stratify_fields"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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131 help="Comma-separated list of FORMAT fields to stratify by"/>
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132 <param argument="--stratify-binsizes" type="text" optional="true" label="stratify_binsizes"
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133 help="Comma-separated list of min:max:binsize to stratify each field on. Must be same length as --stratify-fields."/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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134 <param argument="--stratify-file" type="integer" optional="true" label="stratify_file"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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135 help="Set to 1 to stratify based on --vcf1. Set to 2 to stratify based on --vcf2. Set to 0 to apply stratification to both --vcf1 and --vcf2"/>
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136 <param argument="--period" type="boolean" optional="true" label="period"
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137 help="Report results overall and also stratified by repeat unit length (period)"/>
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138 </section>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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139 <section name="plotting_options" title="Plotting options" expanded="false">
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140 <param argument="--bubble-min" type="integer" optional="true" label="bubble_min"
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141 help="Minimum x/y axis value to display on bubble plots"/>
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142 <param argument="--bubble-max" type="integer" optional="true" label="bubble_max"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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143 help="Maximum x/y axis value to display on bubble plots"/>
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144 </section>
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145 <section name="optional_arguments" title="Optional arguments" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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146 <param argument="--verbose" type="boolean" optional="true" label="verbose"
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147 help="Print helpful debugging info"/>
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148 <param argument="--numrecords" type="integer" optional="true" label="numrecords"
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149 help="For debugging, only process this many records"/>
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150 <param argument="--noplot" type="boolean" optional="true" label="noplot"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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151 help="Don't output any plots. Only produce text output"/>
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152 <param argument="--vcftype1" type="select" optional="true" label="vcftype1"
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153 help="Genotyper that was used to create this VCF input">
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154 <expand macro="vcfTypes"/>
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155 </param>
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156 <param argument="--vcftype2" type="select" optional="true" label="vcftype2"
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157 help="Genotyper that was used to create this VCF input">
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158 <expand macro="vcfTypes"/>
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159 </param>
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160 <param argument="--ignore-phasing" type="boolean" optional="true" label="ignore_phasing"
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161 help="Treat all calls as if they are unphased"/>
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162 </section>
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163 <section name="versiondc8f" title="Version" expanded="false">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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164 <param argument="--version" type="boolean" optional="true" label="version"
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165 help="show program's version number and exit"/>
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166 </section>
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167 </inputs>
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168
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169
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170 <outputs>
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171 <data name="stdout" label="STDOUT output" format="txt"/>
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172 <data name="stderr" label="STDERR output" format="txt"/>
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173
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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174 <collection format="pdf" name="pdfOutput" type="list" label="PDF output">
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175 <discover_datasets format="pdf" pattern="(?P&lt;designation&gt;.+)\.pdf"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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176 </collection>
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177
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178 <collection format="tabular" name="tabularOutput" type="list" label="Text file output">
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179 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tab"/>
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180 </collection>
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181 </outputs>
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182
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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183
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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184 <tests>
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185 <test>
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186 <section name="required">
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187 <param name="vcf1" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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188 <param name="vcf2" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
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189 <param name="out" value="test_result"/>
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190 </section>
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191
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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192 <section name="stratification">
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193 <param name="stratify_fields" value="DP,Q"/>
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194 <param name="stratify_binsizes" value="0:50:5,0:1:0.1"/>
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195 <param name="stratify_file" value="0"/>
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196 </section>
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197 <section name="other">
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198 <param name="verbose" value="true"/>
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199 <param name="vcftype1" value="hipstr"/>
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200 <param name="vcftype2" value="hipstr"/>
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201 </section>
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202
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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203 <output name="stdout" file="stdout.txt"/>
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204 <output name="stderr" file="stderr.txt"/>
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205
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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206 <output_collection name="pdfOutput" type="list">
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207 <element name="test_result-bubble-periodALL">
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208 <assert_contents>
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209 <has_size value="24771" delta="200"/>
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210 </assert_contents>
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211 </element>
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212 <element name="test_result-locuscompare">
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213 <assert_contents>
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214 <has_size value="12800" delta="200"/>
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215 </assert_contents>
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216 </element>
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217 <element name="test_result-samplecompare">
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218 <assert_contents>
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219 <has_size value="9247" delta="200"/>
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220 </assert_contents>
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221 </element>
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222
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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223 </output_collection>
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224 <output_collection name="tabularOutput" type="list">
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225 <element name="test_result-overall" file="test_result-overall.tab"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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226 <element name="test_result-locuscompare" file="test_result-locuscompare.tab"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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227 <element name="test_result-samplecompare" file="test_result-samplecompare.tab"/>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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228 </output_collection>
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229 </test>
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230 </tests>
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231
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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232
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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233 <help>usage: main.py [-h] --vcf1 VCF1 --vcf2 VCF2 --out OUT [--samples SAMPLES] [--region REGION] [--stratify-fields
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234 STRATIFY_FIELDS] [--stratify-binsizes STRATIFY_BINSIZES] [--stratify-file STRATIFY_FILE] [--period]
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235 [--bubble-min BUBBLE_MIN] [--bubble-max BUBBLE_MAX] [--verbose] [--numrecords NUMRECORDS] [--noplot] [--vcftype1
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236 VCFTYPE1] [--vcftype2 VCFTYPE2] [--ignore-phasing] [--version]
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237
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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238 options:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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239 -h, --help show this help message and exit
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240
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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241 Required arguments:
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242 --vcf1 VCF1 First VCF file to compare (must be sorted, bgzipped, and indexed)
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243 --vcf2 VCF2 Second VCF file to compare (must be sorted, bgzipped, and indexed)
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244 --out OUT Prefix to name output files
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245
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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246 Filtering options:
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247 --samples SAMPLES File containing list of samples to include
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248 --region REGION Restrict to this region chrom:start-end
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249
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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250 Metrics to stratify results:
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251 --stratify-fields STRATIFY_FIELDS
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252 Comma-separated list of FORMAT fields to stratify by
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253 --stratify-binsizes STRATIFY_BINSIZES
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254 Comma-separated list of min:max:binsize to stratify each field on. Must be same length as --stratify-fields.
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255 --stratify-file STRATIFY_FILE
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256 Set to 1 to stratify based on --vcf1. Set to 2 to stratify based on --vcf2. Set to 0 to apply stratification to
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257 both --vcf1 and --vcf2
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258 --period Report results overall and also stratified by repeat unit length (period)
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259
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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260 Plotting options:
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261 --bubble-min BUBBLE_MIN
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262 Minimum x/y axis value to display on bubble plots
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263 --bubble-max BUBBLE_MAX
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264 Maximum x/y axis value to display on bubble plots
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265
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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266 Optional arguments:
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267 --verbose Print helpful debugging info
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268 --numrecords NUMRECORDS
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269 For debugging, only process this many records
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270 --noplot Don't output any plots. Only produce text output
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271 --vcftype1 VCFTYPE1 ##!!## Name trh could not be loaded
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272 --vcftype2 VCFTYPE2 ##!!## Name trh could not be loaded
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273 --ignore-phasing Treat all calls as if they are unphased
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274
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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275 Version:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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276 --version show program's version number and exit
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277 </help>
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278
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279
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280 <citations>
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281 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats,
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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282 author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek},
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283 year = {2020},
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284 title = {TRTools},
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285 publisher = {GitHub},
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286 journal = {GitHub repository},
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287 url = {https://github.com/gymreklab/trtools},
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288 }
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289 </citation>
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290 </citations>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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291 </tool>