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annotate macros.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
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ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
michal_klinka
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1 <macros>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
michal_klinka
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2 <token name="@tool_version@">4.1.0</token>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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3 <token name="@INDEX_VCFS@"><![CDATA[##prepare input and indices
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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4 #import os
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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5
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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6 #def get_new_vcf_names(vcf_paths):
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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7 #set result = []
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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8 #for $vcf in $vcf_paths:
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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9 #set $split_path = $os.path.basename(vcf)
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
michal_klinka
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10 #set new_file_name = f"tmp_{split_path.split('.')[0]}.vcf.gz"
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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11 $result.append($new_file_name)
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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12 #end for
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13 #return $result
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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14 #end def
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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15 #def index_vcfs(old_paths, new_paths):
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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16 #for ($left, $right) in $zip($old_paths, $new_paths):
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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17 ln -sfn $left $right &&
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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18 tabix -f -p vcf $right &&
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19 #end for
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20 #end def]]></token>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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21 <xml name="requirements">
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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22 <requirements>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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23 <requirement type="package" version="4.1.0">trtools</requirement>
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24 <requirement type="package" version="1.14">samtools</requirement>
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25 </requirements>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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26 </xml>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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27 <xml name="vcfTypes">
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28 <option value="auto">Auto</option>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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29 <option value="gangstr">GangSTR</option>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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30 <option value="advntr">Advntr</option>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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31 <option value="hipstr">HipSTR</option>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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32 <option value="eh">Expansion hunter</option>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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33 <option value="popstr">PopSTR</option>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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34 </xml>
ecf8c4f9f8ba "planemo upload for repository https://github.com/Kulivox/TRToolsGalaxyWrapper commit 08480e3145858e41b14bf1061f87243e8cc2d04e"
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35 </macros>