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
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-1:000000000000 0:ecf8c4f9f8ba
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>