Mercurial > repos > michal_klinka > trtools
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Apr 23 16:34:03 2022 +0000 @@ -0,0 +1,35 @@ +<macros> + <token name="@tool_version@">4.1.0</token> + <token name="@INDEX_VCFS@"><![CDATA[##prepare input and indices +#import os + +#def get_new_vcf_names(vcf_paths): + #set result = [] + #for $vcf in $vcf_paths: + #set $split_path = $os.path.basename(vcf) + #set new_file_name = f"tmp_{split_path.split('.')[0]}.vcf.gz" + $result.append($new_file_name) + #end for + #return $result +#end def +#def index_vcfs(old_paths, new_paths): + #for ($left, $right) in $zip($old_paths, $new_paths): + ln -sfn $left $right && + tabix -f -p vcf $right && + #end for +#end def]]></token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="4.1.0">trtools</requirement> + <requirement type="package" version="1.14">samtools</requirement> + </requirements> + </xml> + <xml name="vcfTypes"> + <option value="auto">Auto</option> + <option value="gangstr">GangSTR</option> + <option value="advntr">Advntr</option> + <option value="hipstr">HipSTR</option> + <option value="eh">Expansion hunter</option> + <option value="popstr">PopSTR</option> + </xml> +</macros>