Search covariance model(s) against a sequence database
macros.xml
128.0
--smxsize $smxsize
#end if
#if $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'
]]>
A is True
`_.
]]>