## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
    ## it will be converted to a tab delimited file and piped to Galaxy
    temp_tabular_output=\$(mktemp) &&

    #if str($cm_opts.cm_opts_selector) == "histdb":
        ln -s '$cm_opts.cmfile' cmdb.cm &&
    #end if

    tar xvf '$aux_files' &&
    ln -s `find *.i1f` cmdb.cm.i1f &&
    ln -s `find *.i1i` cmdb.cm.i1i &&
    ln -s `find *.i1m` cmdb.cm.i1m &&
    ln -s `find *.i1p` cmdb.cm.i1p &&

    cmscan
        --cpu "\${GALAXY_SLOTS:-2}"
        --tblout '\$temp_tabular_output'
        -o /dev/null
        $g
        #if $Z
            -Z $Z
        #end if
        $verbose
        $other_opts.notrunc
        $other_opts.anytrunc
        $other_opts.nonull3
        #if $other_opts.smxsize <> 128.0
            --smxsize $other_opts.smxsize
        #end if
        #if $other_opts.mxsize <> 128.0
            --mxsize $other_opts.mxsize
        #end if
        $other_opts.cyk
        $other_opts.acyk
        $other_opts.bottomonly
        $other_opts.toponly
        #if str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incE":
            --incE $inclusion_thresholds_opts.incE
        #elif str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incT":
            --incT $inclusion_thresholds_opts.incT
        #end if
        #if str($reporting_thresholds_opts.reporting_thresholds_selector) == "-E":
            -E $reporting_thresholds_opts.E
        #elif str($reporting_thresholds_opts.reporting_thresholds_selector) == "-T":
            -T $reporting_thresholds_opts.T
        #end if
        $model_thresholds.cut_ga
        $model_thresholds.cut_nc
        $model_thresholds.cut_tc
        #if $acceleration_huristics.acceleration_huristics_selector == "FZ"
            --FZ $$acceleration_huristics.FZ
        #else
            $acceleration_huristics.acceleration_huristics_selector
            #if $acceleration_huristics.acceleration_huristics_selector == "--mid"
                --Fmid $acceleration_huristics.Fmid
            #end if
        #end if
        ## CM file from the history or stored as database on disc
        #if str($cm_opts.cm_opts_selector) == "db":
            '$cm_opts.database.fields.path'
        #else:
            ##'$cm_opts.cmfile'
            cmdb.cm
        #end if
        ## sequence file
        '$seqdb'
        ######### Parse the output file in order to fix a problem reported in https://help.galaxyproject.org/t/messy-infernal-cmscan-output/5984
        ## remove the header
        && tail -n +3 '\$temp_tabular_output' > headless_file
        ## extract the last column, since the description includes a variable number of spaces (so, is not considered as a column by awk)
        && awk '{$1=$2=$3=$4=$5=$6=$7=$8=$9=$10=$11=$12=$13=$14=$15=$16=$17=""; print $0}' headless_file > description_column
        ## fix the tabulation the rest content (except the description column)
        && awk 'OFS="\t" {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17 > ("tabulated_columns")}' headless_file
        ## add the description column to the tabulated data
        && paste -d"\t" tabulated_columns description_column > joined_file
        ## include a correct header
        && echo -e '#target\tname\taccession\tquery name\taccession\tmdl\tmdl from\tmdl to\tseq from\tseq to\tstrand\ttrunc\tpass\tgc\tbias\tscore\tE-value\tinc\tdescription of target' > header
        ## export the result
        && cat header joined_file > '$outfile'