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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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1 <?xml version="1.0" ?>
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2 <tool id="mergeSTR" name="MergeSTR" version="@tool_version@">
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3 <description>MergeSTR merges multiple VCF files produced by the same TR
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4 genotyper into a single VCF file.
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5 </description>
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6
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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10
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11 <expand macro="requirements"/>
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12 <version_command>mergeSTR --version</version_command>
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13 <command detect_errors="exit_code"><![CDATA[
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14 @INDEX_VCFS@
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15 #set $inputs = [str(vcf['vcf']) for vcf in $required_arguments.vcfs]
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16 #set $temp_inputs = $get_new_vcf_names($inputs)
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17 #set $indexed_inputs_comma_separated = ",".join($temp_inputs)
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18
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19 $index_vcfs($inputs, $temp_inputs)
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20
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21 mergeSTR
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22
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23 ## vcfs definition
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24 #if $required_arguments.vcfs:
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25 --vcfs $indexed_inputs_comma_separated
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26 #end if
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27 ## end vcfs definition
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28 ## out definition
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29 #if $required_arguments.out:
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30 --out $required_arguments.out
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31 #end if
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32 ## end out definition
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33 ## vcftype definition
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34 #if $required_arguments.vcftype:
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35 --vcftype $required_arguments.vcftype
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36 #end if
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37 ## end vcftype definition
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38 ## update_sample_from_file definition
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39 #if $special_merge_options.update_sample_from_file:
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40 --update-sample-from-file
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41 #end if
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42 ## end update_sample_from_file definition
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43 ## verbose definition
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44 #if $optional_arguments.verbose:
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45 --verbose
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46 #end if
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47 ## end verbose definition
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48 ## quiet definition
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49 #if $optional_arguments.quiet:
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50 --quiet
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51 #end if
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52 ## end quiet definition
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53 ## version definition
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54 #if $versione869.version:
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55 --version
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56 #end if
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57 ## end version definition
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58 1>$stdout 2>$stderr
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59 ]]></command>
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60
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61
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62 <inputs>
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63 <section name="required_arguments" title="Required arguments"
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64 expanded="false">
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65 <repeat name="vcfs" title="VCF files to merge">
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66 <param argument="--vcf" type="data" format="vcf_bgzip" label="VCF file" help="VCF file to analyze"/>
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67 </repeat>
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68 <param argument="--out" type="text" optional="false" label="out"
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69 help="Prefix to name output files"/>
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70 <param argument="--vcftype" type="select" optional="true"
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71 label="vcftype"
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72 help="Genotyper that was used to create this VCF input">
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73 <expand macro="vcfTypes"/>
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74 </param>
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75 </section>
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76 <section name="special_merge_options" title="Special merge options"
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77 expanded="false">
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78 <param argument="--update-sample-from-file" type="boolean"
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79 optional="true" label="update_sample_from_file"
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80 help="Use file names, rather than sample header names, when merging"/>
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81 </section>
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82 <section name="optional_arguments" title="Optional arguments"
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83 expanded="false">
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84 <param argument="--verbose" type="boolean" optional="true"
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85 label="verbose" help="Print out extra info"/>
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86 <param argument="--quiet" type="boolean" optional="true"
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87 label="quiet" help="Don't print out anything"/>
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88 </section>
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89 <section name="versione869" title="Version" expanded="false">
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90 <param argument="--version" type="boolean" optional="true"
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91 label="version"
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92 help="show program's version number and exit"/>
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93 </section>
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94 </inputs>
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95
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96
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97 <outputs>
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98 <data name="stdout" label="STDOUT and output files" format="txt">
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99 <discover_datasets format="vcf" pattern="(?P&lt;designation&gt;.+)\.vcf$" visible="true"/>
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100 </data>
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101 <data name="stderr" label="STDERR output" format="txt"/>
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102 </outputs>
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103
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104
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105 <tests>
1
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106 <test>
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107 <section name="required_arguments">
0
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108 <param name="out" value="test_result"/>
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109 <param name="vcftype" value="hipstr"/>
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110 <repeat name="vcfs">
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111 <param name="vcf" value="NA12878_chr21_hipstr.sorted.vcf.gz"/>
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112 </repeat>
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113 <repeat name="vcfs">
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114 <param name="vcf" value="NA12891_chr21_hipstr.sorted.vcf.gz"/>
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115 </repeat>
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116 </section>
1
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117 <section name="optional_arguments">
0
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118 <param name="verbose" value="true"/>
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119 </section>
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120 <output name="stdout" file="stdout.txt">
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121 <discovered_dataset designation="test_result">
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122 <!-- The vcf output itself can't be directly compared, because it contains the command that executed it, and that command is different for every run -->
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123 <assert_contents>
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124 <has_size value="3106435" delta="100"/>
0
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125 <has_text text="##fileformat=VCFv4.1"/>
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126 <has_n_lines n="9658"/>
0
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127 </assert_contents>
1
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128 </discovered_dataset>
0
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129 </output>
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130 <output name="stderr" file="stderr.txt"/>
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131 </test>
0
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132 </tests>
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133
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134
1
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135 <help>sage: pygalgen [-h] --vcfs VCFS --out OUT [--vcftype VCFTYPE] [--update-sample-from-file] [--verbose] [--quiet]
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136 [--version]
0
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137
1
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138 options:
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139 -h, --help show this help message and exit
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140
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141 Required arguments:
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142 --vcfs VCFS Comma-separated list of VCF files to merge (must be sorted, bgzipped and indexed)
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143 --out OUT Prefix to name output files
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144 --vcftype VCFTYPE ##!!## Name trh could not be loaded
0
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145
1
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146 Special merge options:
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147 --update-sample-from-file
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148 Use file names, rather than sample header names, when merging
0
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149
1
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150 Optional arguments:
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151 --verbose Print out extra info
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152 --quiet Don't print out anything
0
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153
1
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154 Version:
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155 --version show program's version number and exit
0
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156 </help>
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157
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158
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159 <citations>
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160 <citation type="bibtex">@misc{TRTools: a toolkit for genome-wide
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161 analysis of tandem repeats,
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162 author = {Nima Mousavi, Jonathan Margoliash, Neha Pusarla, Shubham
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163 Saini, Richard Yanicky, Melissa Gymrek},
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164 year = {2020},
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165 title = {TRTools},
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166 publisher = {GitHub},
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167 journal = {GitHub repository},
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168 url = {https://github.com/gymreklab/trtools},
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169 }
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170 </citation>
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171 </citations>
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172 </tool>