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