## 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) &&

        cmsearch
            ## Infernal Options
            --cpu "\${GALAXY_SLOTS:-2}"
            -o /dev/null
            --tformat $seqdb.ext ##target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip
            $bottomonly
            $toponly
            $cyk
            $acyk
            $notrunc
            $anytrunc
            $nonull3
            #if str($smxsize) != "128.0"
                --smxsize $smxsize
            #end if
            #if str($mxsize) != "128.0"
                --mxsize $mxsize
            #end if
            --tblout \$temp_tabular_output
            $g
            #if $Z
                -Z $Z
            #end if
            #if $A:
                $A '$multiple_alignment_output'
            #end if
            #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:
                $cm_opts.cmfile
            #end if
            ## sequence file
            '$seqdb'
            2>&1
            &&
            ## 1. replace all lines starting # (comment lines)
            ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
            sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' \$temp_tabular_output > '$outfile'