macros.xml

<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>