when launching identification process with tandemng the refine part is not taking in account

Bug report

i'm not sure if it's a bug of tandemng or iémasschroq

Version of X!TandemPipeline

1.0.12 with tandemng 2017

Error message

no error produce but when you looqing at xml result, you see that all refine part is in unused section of parameter

<group label="unused input parameters"  type="parameters">
	<note type="input" label="protein, use minimal annotations">yes</note>
	<note type="input" label="refine, cleavage semi">yes</note>
	<note type="input" label="refine, maximum missed cleavage sites">3</note>
	<note type="input" label="refine, modification mass">57.02146@C</note>
	<note type="input" label="refine, modification mass 1"></note>
	<note type="input" label="refine, modification mass 2"></note>
	<note type="input" label="refine, point mutations">no</note>
	<note type="input" label="refine, potential C-terminus modifications"></note>
	<note type="input" label="refine, potential N-terminus modifications"></note>
	<note type="input" label="refine, potential modification mass">15.99491@M, 15.99491@W, 0.98402@N, 0.98402@Q</note>
	<note type="input" label="refine, potential modification mass 1"></note>
	<note type="input" label="refine, potential modification mass 2"></note>
	<note type="input" label="refine, potential modification motif"></note>
	<note type="input" label="refine, potential modification motif 1"></note>
	<note type="input" label="refine, potential modification motif 2"></note>
	<note type="input" label="refine, unanticipated cleavage">no</note>
	<note type="input" label="refine, use potential modifications for full refinement">yes</note>
	<note type="input" label="residue, modification mass 2"></note>
	<note type="input" label="residue, potential modification mass 1"></note>
	<note type="input" label="residue, potential modification mass 2"></note>
	<note type="input" label="residue, potential modification motif 1"></note>
	<note type="input" label="residue, potential modification motif 2"></note>
	<note type="input" label="scoring, pluggable scoring">no</note>
	<note type="input" label="spectrum, use noise suppression">yes</note>
</group>

File used

/gorgone/pappso/moulon/raw/20240221_marchadier_77

result output in /gorgone/pappso/moulon/users/thierry/20240221_marchadier_77/xml