I've not used this tool but found the underlying code that describes the input column ordering. To make sure the values for the columns are valid for HGVS format, review the file specification at https://varnomen.hgvs.org/.
For use in Galaxy, you may need to assign the datatype
tabular to the input dataset if you haven't done that already. I can't determine if
tabular is required by the tool (or maybe both are accepted). You'll need to test that out. https://galaxyproject.org/support/metadata/
Each $ variable represents a data column in the order expected.
my ($chr_column, $pos_column, $ref_column, $alt_column, $alt_cnt_column, $tot_cnt_column, $dbid_column, $cdna_hgvs_column, $aa_hgvs_column, $transcript_column, $zygosity_column, $caveats_column, $phase_column, $pvalue_column, $genename_column);
Another part of the code that labels the $ variables.
"Chr" => \$chr_column,
"DNA From" => \$pos_column,
"Gene Name" => \$genename_column,
"Ref base" => \$ref_column,
"Obs base" => \$alt_column,
"Variant Reads" => \$alt_cnt_column,
"Total Reads" => \$tot_cnt_column,
"Variant DB ID" => \$dbid_column,
"Transcript HGVS" => \$cdna_hgvs_column,
"Protein HGVS" => \$aa_hgvs_column,
"Selected transcript" => \$transcript_column,
"Zygosity" => \$zygosity_column,
"Caveats" => \$caveats_column,
"Phase" => \$phase_column,
"P-value" => \$pvalue_column);
Thanks! Jen, Galaxy team
MTS Reference: https://toolshed.g2.bx.psu.edu/view/yusuf/hgvs_vcf/138d81f259c8