Mercurial > repos > michal_klinka > trtools
comparison macros.xml @ 0:ecf8c4f9f8ba draft
"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 |
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| -1:000000000000 | 0:ecf8c4f9f8ba |
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| 1 <macros> | |
| 2 <token name="@tool_version@">4.1.0</token> | |
| 3 <token name="@INDEX_VCFS@"><![CDATA[##prepare input and indices | |
| 4 #import os | |
| 5 | |
| 6 #def get_new_vcf_names(vcf_paths): | |
| 7 #set result = [] | |
| 8 #for $vcf in $vcf_paths: | |
| 9 #set $split_path = $os.path.basename(vcf) | |
| 10 #set new_file_name = f"tmp_{split_path.split('.')[0]}.vcf.gz" | |
| 11 $result.append($new_file_name) | |
| 12 #end for | |
| 13 #return $result | |
| 14 #end def | |
| 15 #def index_vcfs(old_paths, new_paths): | |
| 16 #for ($left, $right) in $zip($old_paths, $new_paths): | |
| 17 ln -sfn $left $right && | |
| 18 tabix -f -p vcf $right && | |
| 19 #end for | |
| 20 #end def]]></token> | |
| 21 <xml name="requirements"> | |
| 22 <requirements> | |
| 23 <requirement type="package" version="4.1.0">trtools</requirement> | |
| 24 <requirement type="package" version="1.14">samtools</requirement> | |
| 25 </requirements> | |
| 26 </xml> | |
| 27 <xml name="vcfTypes"> | |
| 28 <option value="auto">Auto</option> | |
| 29 <option value="gangstr">GangSTR</option> | |
| 30 <option value="advntr">Advntr</option> | |
| 31 <option value="hipstr">HipSTR</option> | |
| 32 <option value="eh">Expansion hunter</option> | |
| 33 <option value="popstr">PopSTR</option> | |
| 34 </xml> | |
| 35 </macros> |