infernal: cmsearch.xml annotate

annotate cmsearch.xml @ 7:477d829d3250 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 1527e05bcd748a2b3cef22e0e356697066a55635

author	bgruening
date	Sat, 11 Nov 2017 16:01:09 -0500
parents	6e18e0b098cd
children	c9e29ac5d099

rev	line source
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	1 <tool id="infernal_cmsearch" name="cmsearch" version="@VERSION@.0">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	2 <description>Search covariance model(s) against a sequence database </description>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	3 <macros>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	4 <import>macros.xml</import>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	5 </macros>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	6 <parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	7 <expand macro="requirements"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	8 <expand macro="stdio" />
0 652f9d550531 Uploaded bgruening parents: diff changeset	9 <command>
2 fac157e22e1b Uploaded bgruening parents: 1 diff changeset	10 <![CDATA[
0 652f9d550531 Uploaded bgruening parents: diff changeset	11 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
652f9d550531 Uploaded bgruening parents: diff changeset	12 ## it will be converted to a tab delimited file and piped to Galaxy
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	13 temp_tabular_output=\$(mktemp) &&
0 652f9d550531 Uploaded bgruening parents: diff changeset	14
2 fac157e22e1b Uploaded bgruening parents: 1 diff changeset	15 cmsearch
0 652f9d550531 Uploaded bgruening parents: diff changeset	16 ## Infernal Options
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	17 --cpu "\${GALAXY_SLOTS:-2}"
0 652f9d550531 Uploaded bgruening parents: diff changeset	18 -o /dev/null
2 fac157e22e1b Uploaded bgruening parents: 1 diff changeset	19 --tformat $seqdb.ext ##target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip
0 652f9d550531 Uploaded bgruening parents: diff changeset	20 $bottomonly
652f9d550531 Uploaded bgruening parents: diff changeset	21 $toponly
652f9d550531 Uploaded bgruening parents: diff changeset	22 $cyk
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	23 $acyk
0 652f9d550531 Uploaded bgruening parents: diff changeset	24 $notrunc
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	25 $anytrunc
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	26 $nonull3
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	27 #if $smxsize <> 128.0
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	28 --smxsize $smxsize
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	29 #end if
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	30 #if $mxsize <> 128.0
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	31 --mxsize $mxsize
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	32 #end if
0 652f9d550531 Uploaded bgruening parents: diff changeset	33 --tblout \$temp_tabular_output
652f9d550531 Uploaded bgruening parents: diff changeset	34 $g
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	35 #if $Z
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	36 -Z $Z
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	37 #end if
0 652f9d550531 Uploaded bgruening parents: diff changeset	38 #if $A:
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	39 $A '$multiple_alignment_output'
0 652f9d550531 Uploaded bgruening parents: diff changeset	40 #end if
652f9d550531 Uploaded bgruening parents: diff changeset	41 #if str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incE":
652f9d550531 Uploaded bgruening parents: diff changeset	42 --incE $inclusion_thresholds_opts.incE
652f9d550531 Uploaded bgruening parents: diff changeset	43 #elif str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incT":
652f9d550531 Uploaded bgruening parents: diff changeset	44 --incT $inclusion_thresholds_opts.incT
652f9d550531 Uploaded bgruening parents: diff changeset	45 #end if
652f9d550531 Uploaded bgruening parents: diff changeset	46 #if str($reporting_thresholds_opts.reporting_thresholds_selector) == "-E":
652f9d550531 Uploaded bgruening parents: diff changeset	47 -E $reporting_thresholds_opts.E
652f9d550531 Uploaded bgruening parents: diff changeset	48 #elif str($reporting_thresholds_opts.reporting_thresholds_selector) == "-T":
652f9d550531 Uploaded bgruening parents: diff changeset	49 -T $reporting_thresholds_opts.T
652f9d550531 Uploaded bgruening parents: diff changeset	50 #end if
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	51 $model_thresholds.cut_ga
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	52 $model_thresholds.cut_nc
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	53 $model_thresholds.cut_tc
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	54 #if $acceleration_huristics.acceleration_huristics_selector == "FZ"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	55 --FZ $$acceleration_huristics.FZ
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	56 #else
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	57 $acceleration_huristics.acceleration_huristics_selector
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	58 #if $acceleration_huristics.acceleration_huristics_selector == "--mid"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	59 --Fmid $acceleration_huristics.Fmid
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	60 #end if
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	61 #end if
0 652f9d550531 Uploaded bgruening parents: diff changeset	62 ## CM file from the history or stored as database on disc
652f9d550531 Uploaded bgruening parents: diff changeset	63 #if str($cm_opts.cm_opts_selector) == "db":
652f9d550531 Uploaded bgruening parents: diff changeset	64 $cm_opts.database.fields.path
652f9d550531 Uploaded bgruening parents: diff changeset	65 #else:
652f9d550531 Uploaded bgruening parents: diff changeset	66 $cm_opts.cmfile
652f9d550531 Uploaded bgruening parents: diff changeset	67 #end if
652f9d550531 Uploaded bgruening parents: diff changeset	68 ## sequence file
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	69 '$seqdb'
2 fac157e22e1b Uploaded bgruening parents: 1 diff changeset	70 2>&1
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	71 &&
0 652f9d550531 Uploaded bgruening parents: diff changeset	72 ## 1. replace all lines starting # (comment lines)
652f9d550531 Uploaded bgruening parents: diff changeset	73 ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	74 sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' \$temp_tabular_output > '$outfile'
0 652f9d550531 Uploaded bgruening parents: diff changeset	75
2 fac157e22e1b Uploaded bgruening parents: 1 diff changeset	76 ]]>
0 652f9d550531 Uploaded bgruening parents: diff changeset	77 </command>
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	78 <inputs>
0 652f9d550531 Uploaded bgruening parents: diff changeset	79
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	80 <param name="seqdb" type="data" format="fasta" label="Sequence database"/>
0 652f9d550531 Uploaded bgruening parents: diff changeset	81
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	82 <conditional name="cm_opts">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	83 <param name="cm_opts_selector" type="select" label="Subject covariance models">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	84 <option value="db" selected="True">Locally installed covariance models</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	85 <option value="histdb">Covariance model from your history</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	86 </param>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	87 <when value="db">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	88 <param name="database" type="select" label="Covariance models">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	89 <options from_file="infernal.loc">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	90 <column name="value" index="0"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	91 <column name="name" index="1"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	92 <column name="path" index="2"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	93 </options>
0 652f9d550531 Uploaded bgruening parents: diff changeset	94 </param>
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	95 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	96 <when value="histdb">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	97 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	98 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	99 </conditional>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	100
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	101 <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	102 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	103 <param argument="-Z" type="float" min="0" optional="true" label="Calculate E-values as if the search space size is 'x' megabases (Mb)" help=""/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	104
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	105 <param argument="--bottomonly" truevalue="--bottomonly" falsevalue="" checked="False" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	106 label="Only search the bottom (Crick) strand of target sequences" help="in the sequence database"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	107 <param argument="--toponly" truevalue="--toponly" falsevalue="" checked="False" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	108 label="Only search the top (Watson) strand of target sequences" help="in the sequence database"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	109
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	110 <param argument="--cyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	111 label="Use the CYK algorithm, not Inside, to determine the final score of all hits" help=""/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	112 <param argument="--acyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	113 label="Use the CYK algorithm to align hits" help="By default, the Durbin/Holmes optimal accuracy algorithm is used, which finds the alignment that maximizes the expected accuracy of all aligned residues."/>
0 652f9d550531 Uploaded bgruening parents: diff changeset	114
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	115 <param argument="--notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	116 label="Skip truncated hit detection" help=""/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	117 <param argument="--anytrunc" truevalue="--anytrunc" falsevalue="" checked="false" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	118 label="Allow full and truncated hits anywhere within sequences" help=""/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	119 <param argument="--nonull3" truevalue="--nonull3" falsevalue="" checked="false" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	120 label="Turn off the null3 CM score corrections for biased composition" help="This correction is not used during the HMM filter stages."/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	121 <param argument="--mxsize" type="float" value="128.0" min="0.1"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	122 label="Set the maximum allowable CM DP matrix size to 'x' megabytes" help=""/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	123 <param argument="--smxsize" type="float" value="128.0" min="0.1"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	124 label="Set the maximum allowable CM search DP matrix size to 'x' megabytes." help=""/>
0 652f9d550531 Uploaded bgruening parents: diff changeset	125
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	126 <!-- accelleration pipeline -->
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	127 <conditional name="acceleration_huristics">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	128 <param name="acceleration_huristics_selector" type="select" label="Options controlling acceleration heuristics" help="These options are, in order from least strict (slowest but most sensitive) to most strict (fastest but least sensitive)">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	129 <option value="--max">Turn all heuristic filters off (--max)</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	130 <option value="--nohmm">Skip all HMM filter stages, use only CM (--nohmm)</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	131 <option value="--mid">Skip first two HMM filter stages (SSV and Vit) (--mid)</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	132 <option value="--default" selected="true">Run search space size-dependent pipeline (--default)</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	133 <option value="--rfam">Use a strict filtering strategy devised for large databases (more than 20 Gb) (--rfam)</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	134 <option value="--hmmonly">Use HMM only, don't use a CM at all (--hmmonly)</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	135 <option value="FZ">set filters to defaults used for a search space of size 'x' Mb (--FZ)</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	136 </param>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	137 <when value="--max">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	138 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	139 <when value="--nohmm">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	140 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	141 <when value="--mid">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	142 <param argument="--Fmid" type="float" value="0.02" label="P-value threshold for HMM stages"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	143 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	144 <when value="--default">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	145 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	146 <when value="--rfam">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	147 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	148 <when value="--hmmonly">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	149 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	150 <when value="FZ">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	151 <param argument="--FZ" type="float" value="" label="Size of search space in Mb"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	152 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	153 </conditional>
0 652f9d550531 Uploaded bgruening parents: diff changeset	154
652f9d550531 Uploaded bgruening parents: diff changeset	155
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	156
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	157 <!-- Options for model-specific score thresholding -->
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	158
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	159 <section name="model_thresholds" title="Options controlling model-specific reporting thresholds" help="Curated CM databases may define specific bit score thresholds for each CM, superseding any thresholding based on statistical significance alone.">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	160 <param argument="--cut_ga" truevalue="--cut_ga" falsevalue="" checked="false" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	161 label="Use CM's GA gathering cutoffs as reporting thresholds" help="GA thresholds are generally considered to be the reliable curated thresholds defining family membership"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	162 <param argument="--cut_nc" truevalue="--cut_nc" falsevalue="" checked="false" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	163 label="use CM's NC noise cutoffs as reporting thresholds" help="NC thresholds are generally considered to be the score of the highest-scoring known false positive."/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	164 <param argument="--cut_tc" truevalue="--cut_tc" falsevalue="" checked="false" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	165 label="use CM's TC trusted cutoffs as reporting thresholds" help="TC thresholds are generally considered to be the score of the lowest-scoring known true positive that is above all known false positives."/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	166 </section>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	167
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	168 <!-- Options for inclusion thresholds -->
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	169 <conditional name="inclusion_thresholds_opts">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	170 <param name="inclusion_thresholds_selector" type="select" label="Inclusion thresholds"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	171 help="Inclusion thresholds are stricter than reporting thresholds. Inclusion thresholds control which hits are considered to be reliable enough to be included in an output alignment or in a possible subsequent search round, or marked as significant (”!”) as opposed to questionable (”?”) in hit output.">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	172 <option value="" selected="true">default</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	173 <option value="--incE">Use E-value</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	174 <option value="--incT">Use bit score</option>
0 652f9d550531 Uploaded bgruening parents: diff changeset	175 </param>
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	176 <when value=""/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	177 <when value="--incE">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	178 <param name="incE" type="float" value="0.01" label="Use E-value" help="of <= X as the hit inclusion threshold.">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	179 <sanitizer>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	180 <valid initial="string.printable">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	181 <remove value="'"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	182 </valid>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	183 </sanitizer>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	184 </param>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	185 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	186 <when value="--incT">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	187 <param name="incT" type="integer" value="0" label="Use bit score" help="of >= X as the hit inclusion threshold.">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	188 <sanitizer>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	189 <valid initial="string.printable">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	190 <remove value="'"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	191 </valid>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	192 </sanitizer>
0 652f9d550531 Uploaded bgruening parents: diff changeset	193 </param>
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	194 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	195 </conditional>
0 652f9d550531 Uploaded bgruening parents: diff changeset	196
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	197 <!-- Options controlling reporting thresholds -->
0 652f9d550531 Uploaded bgruening parents: diff changeset	198
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	199 <conditional name="reporting_thresholds_opts">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	200 <param name="reporting_thresholds_selector" type="select" label="reporting thresholds"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	201 help="Reporting thresholds control which hits are reported in output files">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	202 <option value="" selected="true">default</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	203 <option value="-E">Use E-value</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	204 <option value="-T">Use bit score</option>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	205 </param>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	206 <when value=""/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	207 <when value="-E">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	208 <param name="E" type="float" value="10.0" label="Use E-value" help="of <= X as the hit reporting threshold. The default is 10.0, meaning that on average, about 10 false positives will be reported per query, so you can see the top of the noise and decide for yourself if it’s really noise.">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	209 <sanitizer>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	210 <valid initial="string.printable">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	211 <remove value="'"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	212 </valid>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	213 </sanitizer>
0 652f9d550531 Uploaded bgruening parents: diff changeset	214 </param>
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	215 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	216 <when value="-T">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	217 <param name="T" type="integer" value="0" label="Use bit score" help="of >= X as the hit reporting threshold.">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	218 <sanitizer>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	219 <valid initial="string.printable">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	220 <remove value="'"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	221 </valid>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	222 </sanitizer>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	223 </param>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	224 </when>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	225 </conditional>
0 652f9d550531 Uploaded bgruening parents: diff changeset	226
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	227 <param argument="-A" truevalue="-A" falsevalue="" checked="False" type="boolean"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	228 label="Save a multiple alignment of all significant hits" help="... those satisfying inclusion thresholds"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	229 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" checked="false"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	230 label="Omit the alignment section from the main input" help="This can greatly reduce the output volume"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	231 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false"
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	232 label="Include extra search pipeline statistics in the main output" help="They include filter survival statistics for truncated hit detection and number of envelopes discarded due to matrix size overflows."/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	233 </inputs>
0 652f9d550531 Uploaded bgruening parents: diff changeset	234 <outputs>
652f9d550531 Uploaded bgruening parents: diff changeset	235
652f9d550531 Uploaded bgruening parents: diff changeset	236 <data format="tabular" name="outfile" label="cmsearch on ${on_string}"/>
652f9d550531 Uploaded bgruening parents: diff changeset	237 <data format="tabular" name="multiple_alignment_output" label="cmsearch on ${on_string} (multi alignment)">
652f9d550531 Uploaded bgruening parents: diff changeset	238 <filter>A is True</filter>
652f9d550531 Uploaded bgruening parents: diff changeset	239 </data>
652f9d550531 Uploaded bgruening parents: diff changeset	240
652f9d550531 Uploaded bgruening parents: diff changeset	241 </outputs>
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	242 <tests>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	243 <test>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	244 <conditional name="cm_opts">
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	245 <param name="cm_opts_selector" value="histdb"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	246 <param name="cmfile" value="cmsearch_input1.cm"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	247 </conditional>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	248 <param name="seqdb" value="cmsearch_input2.fa"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	249 <output name="outfile" file="cmsearch_result.tabular"/>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	250
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	251 </test>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	252 </tests>
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	253
0 652f9d550531 Uploaded bgruening parents: diff changeset	254 <help>
2 fac157e22e1b Uploaded bgruening parents: 1 diff changeset	255 <![CDATA[
0 652f9d550531 Uploaded bgruening parents: diff changeset	256
652f9d550531 Uploaded bgruening parents: diff changeset	257
652f9d550531 Uploaded bgruening parents: diff changeset	258 What it does
652f9d550531 Uploaded bgruening parents: diff changeset	259
3 2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	260 cmsearch belongs to the INFERNAL software package that allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments.
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	261 You can use your model to search for new homologues of your RNA family. cmsearch is used to search one or more covariance models (CMs) against a sequence database. cmsearch searches both strands of each sequence in the target database, and returns alignments for high scoring hits.
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	262
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	263 To build CMs from multiple alignments, see cmbuild (build covariance models).
0 652f9d550531 Uploaded bgruening parents: diff changeset	264
3 2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	265
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	266 Input
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	267
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	268 The CM query file must have been calibrated for E-values with cmcalibrate. As a special exception, any models CM query files that have zero basepairs need not be calibrated.
0 652f9d550531 Uploaded bgruening parents: diff changeset	269
652f9d550531 Uploaded bgruening parents: diff changeset	270
3 2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	271 Options
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	272
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	273 - Turn on the glocal alignment algorithm: global with respect to the query model and local with respect to the target database. By default, the local alignment algorithm is used which is local with respect to both the target sequence and the model. In local mode, the alignment to span two or more subsequences if necessary (e.g. if the structures of the query model and target sequence are only partially shared), allowing certain large insertions and deletions in the structure to be penalized differently than normal indels. Local mode performs better on empirical benchmarks and is significantly more sensitive for remote homology detection. Empirically, glocal searches return many fewer hits than local searches, so glocal may be desired for some applications. With Turn on the glocal alignment algorithm, all models must be calibrated, even those with zero basepairs.
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	274
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	275 - Only search the bottom (Crick) strand of target sequences: Hits can occur on either the top (Watson) or bottom (Crick) strand of the target sequence. By default, both strands are searched.
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	276
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	277 - Only search the top (Watson) strand of target sequences: Hits can occur on either the top (Watson) or bottom (Crick) strand of the target sequence. By default, both strands are searched.
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	278
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	279 - Use the CYK algorithm, not Inside, to determine the final score of all hits: If selecting "yes", the CYK algorithm instead of the CM Inside algorithm (the SCFG analog of the HMM Forward algorithm) is used.
0 652f9d550531 Uploaded bgruening parents: diff changeset	280
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	281 - Use the CYK algorithm to align hits: By default, the Durbin/Holmes optimal accuracy algorithm is used, which finds the alignment that maximizes the expected accuracy of all aligned residues.
3 2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	282
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	283 - Turn off truncated hit detection: Turns off truncated hit detection and will reduce the running time most significantly for target files that include many short sequences.
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	284
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	285 - Turn off all filters, and run non-banded Inside on every full-length target sequence: This increases sensitivity somewhat, at an extremely large cost in speed.
3 2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	286
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	287 - Turn off all HMM filter stages: The CYK filter, using QDBs, will be run on every full-length target sequence and will enforce a P-value threshold of 0.0001. Each subsequence that survives CYK will be passed to Inside, which will also use QDBs (but a looser set). This increases sensitivity somewhat, at a very large cost in speed.
2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	288
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	289 - Turn off the HMM SSV and Viterbi filter stages:Sets remaining HMM filter thresholds to 0.02 by default. This may increase sensitivity, at a significant cost in speed.
3 2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	290
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	291 - Inclusion thresholds: Use E-value - Use an E-value as the hit inclusion threshold. The default is 0.01, meaning that on average, about 1 false positive would be expected in every 100 searches with different query sequences. Use Bit Score - Instead of using E-values for setting the inclusion threshold, instead use a bit score as the hit inclusion threshold. By default this option is unset.
0 652f9d550531 Uploaded bgruening parents: diff changeset	292
652f9d550531 Uploaded bgruening parents: diff changeset	293
3 2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	294 Output Options
0 652f9d550531 Uploaded bgruening parents: diff changeset	295
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	296 - reporting thresholds: Hits are ranked by statistical significance (E-value). By default, all hits with an E-value <= 10 are reported. The following options allow you to change the default E-value reporting thresholds, or to use bit score thresholds instead.
0 652f9d550531 Uploaded bgruening parents: diff changeset	297
652f9d550531 Uploaded bgruening parents: diff changeset	298
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	299 Output columns:
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	300
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	301 (1) rank
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	302
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	303 (2) E-value
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	304
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	305 (3) score
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	306
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	307 (4) bias
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	308
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	309 (5) sequence
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	310
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	311 (6) start
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	312
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	313 (7) end
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	314
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	315 (8) mdl
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	316
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	317 (9) trunc
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	318
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	319 (10) gc
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	320
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	321 (11) description
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	322
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	323 ---- --------- ------ ----- ----------- ------- ------- --- ----- ---- -----------
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	324
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	325 ! 1.3e-18 71.5 0.0 NC_013790.1 362026 361955 - cm no 0.50 Methanobrevibacter ruminantium M1
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	326
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	327 ! 3.3e-18 70.2 0.0 NC_013790.1 2585265 2585193 - cm no 0.60 Methanobrevibacter ruminantium M1
3 2c2c5e5e495b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty bgruening parents: 2 diff changeset	328
0 652f9d550531 Uploaded bgruening parents: diff changeset	329
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	330 For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.
0 652f9d550531 Uploaded bgruening parents: diff changeset	331
2 fac157e22e1b Uploaded bgruening parents: 1 diff changeset	332 ]]>
0 652f9d550531 Uploaded bgruening parents: diff changeset	333 </help>
5 6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	334 <expand macro="citations" />
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	335
6e18e0b098cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86 bgruening parents: 3 diff changeset	336
0 652f9d550531 Uploaded bgruening parents: diff changeset	337 </tool>

Mercurial > repos > bgruening > infernal

annotate cmsearch.xml @ 7:477d829d3250 draft