Wrapper bug: metaphlan 4.0.6+galaxy2

[jennaj]

tool_id toolshed.g2.bx.psu.edu/repos/iuc/metaphlan/metaphlan/4.0.6+galaxy2

Tool wrapper includes

       <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue='' 

But when that option is used, stderr reports this

Maybe some prior update changed unclassified_estimation from the original unknown_estimation?

usage: metaphlan --input_type {fastq,fasta,bowtie2out,sam} [--force]
[--bowtie2db METAPHLAN_BOWTIE2_DB] [-x INDEX]
[--bt2_ps BowTie2 presets] [--bowtie2_exe BOWTIE2_EXE]
[--bowtie2_build BOWTIE2_BUILD] [--bowtie2out FILE_NAME]
[--min_mapq_val MIN_MAPQ_VAL] [--no_map] [--tmp_dir]
[--tax_lev TAXONOMIC_LEVEL] [--min_cu_len]
[--min_alignment_len] [--add_viruses] [--ignore_eukaryotes]
[--ignore_bacteria] [--ignore_archaea] [--ignore_ksgbs]
[--ignore_usgbs] [--stat_q] [--perc_nonzero]
[--ignore_markers IGNORE_MARKERS] [--avoid_disqm] [--stat]
[-t ANALYSIS TYPE] [--nreads NUMBER_OF_READS]
[--pres_th PRESENCE_THRESHOLD] [--clade] [--min_ab]
[-o output file] [--sample_id_key name]
[--use_group_representative] [--sample_id value]
[-s sam_output_file] [--legacy-output] [--CAMI_format_output]
[--unclassified_estimation] [--mpa3] [--biom biom_output]
[--mdelim mdelim] [--nproc N] [--subsampling SUBSAMPLING]
[--subsampling_seed SUBSAMPLING_SEED] [--install] [--offline]
[--force_download] [--read_min_len READ_MIN_LEN] [-v] [-h]
[INPUT_FILE] [OUTPUT_FILE]
metaphlan: error: unrecognized arguments: --unknown_estimation

Reported at https://help.galaxyproject.org/t/metaphlan-issue-with-unknown-estimation-parameter/12157

[SaimMomin12]

Hi @jennaj,

The bug issue reported above has been fixed now in #5979

Cheers!