Mercurial > repos > michal_klinka > trtools

annotate qcSTR/qcSTR.xml @ 1:8e8cf43f6836 draft default tip

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planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit df706bf76531920d935ec6d2eb41b9b1420aa390
author michal_klinka
date Sun, 15 May 2022 15:23:59 +0000
parents ecf8c4f9f8ba
children
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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" ?>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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2 <tool id="qcSTR" name="QcSTR" version="@tool_version@">
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3 <description>qcSTR generates plots that are useful for diagnosing issues in TR calling.</description>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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4 <macros>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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5 <import>macros.xml</import>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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6 </macros>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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7 <expand macro="requirements"/>
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8 <version_command>qcSTR --version</version_command>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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9 <command detect_errors="exit_code"><![CDATA[qcSTR
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10
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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11 ## vcf definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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12 #if $required_arguments.vcf:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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13 --vcf $required_arguments.vcf
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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14 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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15 ## end vcf definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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16 ## out definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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17 #if $required_arguments.out:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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18 --out $required_arguments.out
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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19 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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20 ## end out definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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21 ## vcftype definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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22 #if $optional_input_arguments.vcftype:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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23 --vcftype $optional_input_arguments.vcftype
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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24 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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25 ## end vcftype definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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26 ## samples definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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27 #if $optional_input_arguments.samples:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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28 --samples $optional_input_arguments.samples
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 samples definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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31 ## period definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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32 #if $optional_input_arguments.period:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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33 --period $optional_input_arguments.period
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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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 period definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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36 ## quality_repeat definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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37 #for $item in $quality_plot_options.quality_repeat:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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38 ## quality definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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39 #if $item.quality:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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40 --quality
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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41 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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42 ## end quality definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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43
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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44 #end for
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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45 ## end quality_repeat definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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46 ## quality_ignore_no_call definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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47 #if $quality_plot_options.quality_ignore_no_call:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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48 --quality-ignore-no-call
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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49 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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50 ## end quality_ignore_no_call definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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51 ## refbias_metric definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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52 #if $reference_bias_plot_options.refbias_metric:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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53 --refbias-metric $reference_bias_plot_options.refbias_metric
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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54 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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55 ## end refbias_metric definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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56 ## refbias_mingts definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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57 #if $reference_bias_plot_options.refbias_mingts:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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58 --refbias-mingts $reference_bias_plot_options.refbias_mingts
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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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 refbias_mingts definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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61 ## refbias_xrange_min definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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62 #if $reference_bias_plot_options.refbias_xrange_min:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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63 --refbias-xrange-min $reference_bias_plot_options.refbias_xrange_min
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 refbias_xrange_min definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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66 ## refbias_xrange_max definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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67 #if $reference_bias_plot_options.refbias_xrange_max:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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68 --refbias-xrange-max $reference_bias_plot_options.refbias_xrange_max
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 refbias_xrange_max definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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71 ## refbias_binsize definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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72 #if $reference_bias_plot_options.refbias_binsize:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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73 --refbias-binsize $reference_bias_plot_options.refbias_binsize
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 refbias_binsize definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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76 ## numrecords definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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77 #if $debug_group.numrecords:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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78 --numrecords $debug_group.numrecords
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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79 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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80 ## end numrecords definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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81 ## version definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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82 #if $version05e4.version:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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83 --version
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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84 #end if
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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85 ## end version definition
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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86 1>$stdout 2>$stderr
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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87 ]]></command>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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88
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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89
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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90 <inputs>
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91 <section name="required_arguments" title="Required arguments" expanded="false">
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92 <param argument="--vcf" type="data" format="vcf" optional="false" label="vcf" help="VCF file to analyze."/>
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93 <param argument="--out" type="text" optional="false" label="out" help="Output prefix for files generated"/>
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94 </section>
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95 <section name="optional_input_arguments" title="Optional input arguments" expanded="false">
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96 <param argument="--vcftype" type="select" optional="true" label="vcftype" help="Genotyper that was used to create this VCF input">
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97 <expand macro="vcfTypes"/>
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98 </param>
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99 <param argument="--samples" type="text" optional="true" label="samples" help="File containing list of samples to include"/>
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100 <param argument="--period" type="integer" optional="true" label="period" help="Only consider repeats with this motif length"/>
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101 </section>
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102 <section name="quality_plot_options" title="Quality plot options" expanded="false">
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103 <repeat name="quality_repeat" title="quality_repeat">
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104 <param argument="--quality" type="boolean" optional="true" label="quality" help="Which quality plot(s) to produce. May be specified more than once. See the README for more info">
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105 <option value="per-locus">Per-locus</option>
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106 <option value="sample-stratified">Sample-stratified</option>
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107 <option value="per-sample">Per-sample</option>
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108 <option value="locus-stratified">Locus-stratified</option>
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109 <option value="per-call">Per-call</option>
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110 </param>
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111 </repeat>
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112 <param argument="--quality-ignore-no-call" type="boolean" optional="true" label="quality_ignore_no_call" help="Exclude no-calls and calls without quality scores from quality graph distributions instead of the default, which is to include them as zero quality calls. Setting this can cause the plotting to crash if it reduces the number of valid calls (in a strata) to &lt;= 1"/>
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113 </section>
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114 <section name="reference_bias_plot_options" title="Reference bias plot options" expanded="false">
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115 <param argument="--refbias-metric" type="text" optional="true" label="refbias_metric" help="Which metric to use for the y-axis on the reference bias plot.">
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116 <option value="mean">Mean</option>
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117 <option value="median">Median</option>
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118 </param>
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119 <param argument="--refbias-mingts" type="integer" optional="true" label="refbias_mingts" help="Don't compute points for the reference bias plot based on fewer than this many genotypes"/>
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120 <param argument="--refbias-xrange-min" type="integer" optional="true" label="refbias_xrange_min" help="Minimum x-axis value (bp) to show on the reference bias plot"/>
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121 <param argument="--refbias-xrange-max" type="integer" optional="true" label="refbias_xrange_max" help="Maximum x-axis value (bp) to show on the reference bias plot"/>
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122 <param argument="--refbias-binsize" type="integer" optional="true" label="refbias_binsize" help="Size (bp) of x-axis bins for the reference bias plot"/>
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123 </section>
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124 <section name="debug_group" title="Debug group" expanded="false">
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125 <param argument="--numrecords" type="integer" optional="true" label="numrecords" help="Only process this many records"/>
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126 </section>
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127 <section name="version05e4" title="Version" expanded="false">
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128 <param argument="--version" type="boolean" optional="true" label="version" help="show program's version number and exit"/>
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129 </section>
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130 </inputs>
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131
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132
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133 <outputs>
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134 <data name="stdout" format="txt" />
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135 <data name="stderr" format="txt" />
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136 <collection format="pdf" name="qcSTROutput" type="list" label="Output of qcSTR">
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137 <discover_datasets format="pdf" pattern="(?P&lt;designation&gt;.+)\.pdf"/>
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138 </collection>
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139 </outputs>
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140
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141
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142 <tests>
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143 <test>
1
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144 <section name="required_arguments">
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145 <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
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146 <param name="out" value="test"/>
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147 </section>
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148 <section name="optional_input_arguments">
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149 <param name="vcftype" value="hipstr"/>
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150 </section>
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151
0
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152 <output name="stdout" file="output.txt" />
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153 <output_collection name="qcSTROutput" type="list" count="3">
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154 <element name="test-diffref-bias" ftype="pdf">
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155 <assert_contents>
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156 <has_size value="12600" delta="300" />
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157 <has_text text="%PDF" />
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158 <has_text text="%%EOF" />
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159 </assert_contents>
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160 </element>
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161 <element name="test-diffref-histogram" ftype="pdf">
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162 <assert_contents>
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163 <has_size value="11400" delta="300" />
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164 <has_text text="%PDF" />
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165 <has_text text="%%EOF" />
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166 </assert_contents>
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167 </element>
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168 <element name="test-quality" ftype="pdf">
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169 <assert_contents>
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170 <has_size value="11900" delta="300" />
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171 <has_text text="%PDF" />
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172 <has_text text="%%EOF" />
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173 </assert_contents>
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174 </element>
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175 </output_collection>
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176 </test>
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177 </tests>
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178
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179
1
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180 <help>usage: pygalgen [-h] --vcf VCF --out OUT [--vcftype VCF_TYPE] [--samples SAMPLES]
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181 [--period PERIOD] [--quality {per-locus,sample-stratified,per-sample,locus-stratified,per-call}]
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182 [--quality-ignore-no-call] [--refbias-metric {mean,median}] [--refbias-mingts REFBIAS_MINGTS]
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183 [--refbias-xrange-min REFBIAS_XRANGE_MIN] [--refbias-xrange-max REFBIAS_XRANGE_MAX]
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184 [--refbias-binsize REFBIAS_BINSIZE] [--numrecords NUMRECORDS] [--version]
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185
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186 options:
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187 -h, --help show this help message and exit
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188
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189 Required arguments:
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190 --vcf VCF VCF file to analyze.
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191 --out OUT Output prefix for files generated
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192
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193 Optional input arguments:
1
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194 --vcftype VCF_TYPE Which type of VCF to restrict the input to, or 'auto' for no restrction
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195 --samples SAMPLES File containing list of samples to include
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196 --period PERIOD Only consider repeats with this motif length
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197
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198 Quality plot options:
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199 --quality QUALITY Which quality plot(s) to produce. May be specified more than once. See the README for more
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200 info (per-locus,sample-stratified,per-sample,locus-stratified,per-call)
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201 --quality-ignore-no-call
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202 Exclude no-calls and calls without quality scores from quality graph distributions instead of
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203 the default, which is to include them as zero quality calls. Setting this can cause the
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204 plotting to crash if it reduces the number of valid calls (in a strata) to &lt;= 1
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205
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206 Reference bias plot options:
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207 --refbias-metric METRIC
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208 Which metric to use for the y-axis on the reference bias plot. (mean,median)
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209 --refbias-mingts REFBIAS_MINGTS
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210 Don't compute points for the reference bias plot based on fewer than this many genotypes
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211 --refbias-xrange-min REFBIAS_XRANGE_MIN
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212 Minimum x-axis value (bp) to show on the reference bias plot
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213 --refbias-xrange-max REFBIAS_XRANGE_MAX
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214 Maximum x-axis value (bp) to show on the reference bias plot
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215 --refbias-binsize REFBIAS_BINSIZE
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216 Size (bp) of x-axis bins for the reference bias plot
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217
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218 Debug group:
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219 --numrecords NUMRECORDS
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220 Only process this many records
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221
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222 Version:
1
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223 --version show program's version number and exit</help>
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224
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225
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226 <citations>
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227 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide analysis of tandem repeats,
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228 author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham Saini, Richard Yanicky, Melissa Gymrek},
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229 year = {2020},
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230 title = {TRTools},
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231 publisher = {GitHub},
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232 journal = {GitHub repository},
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233 url = {https://github.com/gymreklab/trtools},
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234 }</citation>
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235 </citations>
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236 </tool>