Mercurial > repos > bgruening > infernal
annotate cmscan.xml @ 19:94cc7ef25867 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
| author | bgruening |
|---|---|
| date | Thu, 23 Sep 2021 19:38:15 +0000 |
| parents | 0ac29b4bb1cb |
| children | b10f7688d14c |
| rev | line source |
|---|---|
|
19
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
1 <tool id="infernal_cmscan" name="cmscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
|
16
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
2 <description> Search sequences against collections of covariance models</description> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
3 <macros> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
4 <import>macros.xml</import> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
5 </macros> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
6 <expand macro="requirements"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
7 <expand macro="stdio"/> |
|
19
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
8 <expand macro="xrefs"/> |
|
16
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
9 <command> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
10 <![CDATA[ |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
11 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
12 ## it will be converted to a tab delimited file and piped to Galaxy |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
13 temp_tabular_output=\$(mktemp) && |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
14 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
15 #if str($cm_opts.cm_opts_selector) == "histdb": |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
16 ln -s '$cm_opts.cmfile' cmdb.cm && |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
17 #end if |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
18 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
19 tar xvf '$aux_files' && |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
20 ln -s `find *.i1f` cmdb.cm.i1f && |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
21 ln -s `find *.i1i` cmdb.cm.i1i && |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
22 ln -s `find *.i1m` cmdb.cm.i1m && |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
23 ln -s `find *.i1p` cmdb.cm.i1p && |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
24 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
25 cmscan |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
26 --cpu "\${GALAXY_SLOTS:-2}" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
27 --tblout '\$temp_tabular_output' |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
28 -o /dev/null |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
29 $g |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
30 #if $Z |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
31 -Z $Z |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
32 #end if |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
33 $verbose |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
34 $other_opts.notrunc |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
35 $other_opts.anytrunc |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
36 $other_opts.nonull3 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
37 #if $other_opts.smxsize <> 128.0 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
38 --smxsize $other_opts.smxsize |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
39 #end if |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
40 #if $other_opts.mxsize <> 128.0 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
41 --mxsize $other_opts.mxsize |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
42 #end if |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
43 $other_opts.cyk |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
44 $other_opts.acyk |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
45 $other_opts.bottomonly |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
46 $other_opts.toponly |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
47 #if str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incE": |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
48 --incE $inclusion_thresholds_opts.incE |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
49 #elif str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incT": |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
50 --incT $inclusion_thresholds_opts.incT |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
51 #end if |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
52 #if str($reporting_thresholds_opts.reporting_thresholds_selector) == "-E": |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
53 -E $reporting_thresholds_opts.E |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
54 #elif str($reporting_thresholds_opts.reporting_thresholds_selector) == "-T": |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
55 -T $reporting_thresholds_opts.T |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
56 #end if |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
57 $model_thresholds.cut_ga |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
58 $model_thresholds.cut_nc |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
59 $model_thresholds.cut_tc |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
60 #if $acceleration_huristics.acceleration_huristics_selector == "FZ" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
61 --FZ $$acceleration_huristics.FZ |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
62 #else |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
63 $acceleration_huristics.acceleration_huristics_selector |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
64 #if $acceleration_huristics.acceleration_huristics_selector == "--mid" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
65 --Fmid $acceleration_huristics.Fmid |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
66 #end if |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
67 #end if |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
68 ## CM file from the history or stored as database on disc |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
69 #if str($cm_opts.cm_opts_selector) == "db": |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
70 '$cm_opts.database.fields.path' |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
71 #else: |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
72 ##'$cm_opts.cmfile' |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
73 cmdb.cm |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
74 #end if |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
75 ## sequence file |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
76 '$seqdb' |
|
19
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
77 ######### Parse the output file in order to fix a problem reported in https://help.galaxyproject.org/t/messy-infernal-cmscan-output/5984 |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
78 ## remove the header |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
79 && tail -n +3 '\$temp_tabular_output' > headless_file |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
80 ## extract the last column, since the description includes a variable number of spaces (so, is not considered as a column by awk) |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
81 && awk '{$1=$2=$3=$4=$5=$6=$7=$8=$9=$10=$11=$12=$13=$14=$15=$16=$17=""; print $0}' headless_file > description_column |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
82 ## fix the tabulation the rest content (except the description column) |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
83 && awk 'OFS="\t" {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17 > ("tabulated_columns")}' headless_file |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
84 ## add the description column to the tabulated data |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
85 && paste -d"\t" tabulated_columns description_column > joined_file |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
86 ## include a correct header |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
87 && echo -e '#target\tname\taccession\tquery name\taccession\tmdl\tmdl from\tmdl to\tseq from\tseq to\tstrand\ttrunc\tpass\tgc\tbias\tscore\tE-value\tinc\tdescription of target' > header |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
88 ## export the result |
|
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
89 && cat header joined_file > '$outfile' |
|
16
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
90 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
91 ]]> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
92 </command> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
93 <inputs> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
94 <param name="seqdb" type="data" format="fasta" label="Sequence database <seqfile>"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
95 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
96 <conditional name="cm_opts"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
97 <param name="cm_opts_selector" type="select" label="Subject covariance models <cmdb> "> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
98 <option value="db" >Locally installed covariance models</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
99 <option value="histdb" selected="True">Covariance model from your history</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
100 </param> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
101 <when value="db"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
102 <param name="database" type="select" label="Covariance models"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
103 <options from_file="infernal.loc"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
104 <column name="value" index="0"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
105 <column name="name" index="1"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
106 <column name="path" index="2"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
107 </options> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
108 </param> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
109 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
110 <when value="histdb"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
111 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
112 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
113 </conditional> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
114 <param name="aux_files" type="data" format="tar" label="Auxillury files" help="A tar file contains the four auxillury files suffixed .i1{fimp}. These files are generated after pressing the cm files using cmpress"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
115 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
116 <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
117 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
118 <param argument="-Z" type="float" optional="true" min="0" label="Search space size in *Mb* for E-value calculations" help="Without the use of this option, the search space size changes for each query sequence"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
119 <param argument="--verbose" truevalue="--verbose" falsevalue="" checked="False" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
120 label="Be verbose" help="report extra information; mainly useful for debugging"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
121 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
122 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
123 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
124 <!-- Options for inclusion thresholds --> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
125 <conditional name="inclusion_thresholds_opts"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
126 <param name="inclusion_thresholds_selector" type="select" label="Inclusion thresholds" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
127 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."> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
128 <option value="" selected="true">default</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
129 <option value="--incE">Use E-value</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
130 <option value="--incT">Use bit score</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
131 </param> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
132 <when value=""/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
133 <when value="--incE"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
134 <param name="incE" type="float" value="0.01" label="Use E-value" help="of <= X as the hit inclusion threshold."> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
135 <sanitizer> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
136 <valid initial="string.printable"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
137 <remove value="'"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
138 </valid> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
139 </sanitizer> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
140 </param> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
141 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
142 <when value="--incT"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
143 <param name="incT" type="integer" value="0" label="Use bit score" help="of >= X as the hit inclusion threshold."> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
144 <sanitizer> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
145 <valid initial="string.printable"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
146 <remove value="'"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
147 </valid> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
148 </sanitizer> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
149 </param> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
150 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
151 </conditional> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
152 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
153 <!-- Options controlling reporting thresholds --> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
154 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
155 <conditional name="reporting_thresholds_opts"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
156 <param name="reporting_thresholds_selector" type="select" label="reporting thresholds" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
157 help="Reporting thresholds control which hits are reported in output files"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
158 <option value="" selected="true">default</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
159 <option value="-E">Use E-value</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
160 <option value="-T">Use bit score</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
161 </param> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
162 <when value=""/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
163 <when value="-E"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
164 <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."> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
165 <sanitizer> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
166 <valid initial="string.printable"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
167 <remove value="'"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
168 </valid> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
169 </sanitizer> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
170 </param> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
171 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
172 <when value="-T"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
173 <param name="T" type="integer" value="0" label="Use bit score" help="of >= X as the hit reporting threshold."> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
174 <sanitizer> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
175 <valid initial="string.printable"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
176 <remove value="'"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
177 </valid> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
178 </sanitizer> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
179 </param> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
180 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
181 </conditional> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
182 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
183 <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."> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
184 <param argument="--cut_ga" truevalue="--cut_ga" falsevalue="" checked="false" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
185 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"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
186 <param argument="--cut_nc" truevalue="--cut_nc" falsevalue="" checked="false" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
187 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."/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
188 <param argument="--cut_tc" truevalue="--cut_tc" falsevalue="" checked="false" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
189 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."/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
190 </section> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
191 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
192 <conditional name="acceleration_huristics"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
193 <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)"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
194 <option value="--max">Turn all heuristic filters off (--max)</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
195 <option value="--nohmm">Skip all HMM filter stages, use only CM (--nohmm)</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
196 <option value="--mid">Skip first two HMM filter stages (SSV and Vit) (--mid)</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
197 <option value="--default" selected="true">Run search space size-dependent pipeline (--default)</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
198 <option value="--rfam">Use a strict filtering strategy devised for large databases (more than 20 Gb) (--rfam)</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
199 <option value="--hmmonly">Use HMM only, don't use a CM at all (--hmmonly)</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
200 <option value="FZ">set filters to defaults used for a search space of size 'x' Mb (--FZ)</option> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
201 </param> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
202 <when value="--max"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
203 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
204 <when value="--nohmm"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
205 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
206 <when value="--mid"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
207 <param argument="--Fmid" type="float" value="0.02" label="P-value threshold for HMM stages"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
208 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
209 <when value="--default"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
210 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
211 <when value="--rfam"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
212 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
213 <when value="--hmmonly"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
214 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
215 <when value="FZ"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
216 <param argument="--FZ" type="float" value="125" label="Size of search space in Mb"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
217 </when> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
218 </conditional> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
219 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
220 <section name="other_opts" title="Other options"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
221 <param argument="--notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
222 label="Skip truncated hit detection" help=""/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
223 <param argument="--anytrunc" truevalue="--anytrunc" falsevalue="" checked="false" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
224 label="Allow full and truncated hits anywhere within sequences" help=""/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
225 <param argument="--nonull3" truevalue="--nonull3" falsevalue="" checked="false" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
226 label="Turn off the null3 CM score corrections for biased composition" help="This correction is not used during the HMM filter stages."/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
227 <param argument="--mxsize" type="float" value="128.0" min="0.1" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
228 label="Set the maximum allowable CM DP matrix size to 'x' megabytes" help=""/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
229 <param argument="--smxsize" type="float" value="128.0" min="0.1" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
230 label="Set the maximum allowable CM search DP matrix size to 'x' megabytes." help=""/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
231 <param argument="--cyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
232 label="Use the CYK algorithm, not Inside, to determine the final score of all hits" help=""/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
233 <param argument="--acyk" truevalue="--cyk" falsevalue="" checked="False" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
234 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."/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
235 <param argument="--bottomonly" truevalue="--bottomonly" falsevalue="" checked="False" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
236 label="Only search the bottom (Crick) strand of target sequences" help="in the sequence database"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
237 <param argument="--toponly" truevalue="--toponly" falsevalue="" checked="False" type="boolean" |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
238 label="Only search the top (Watson) strand of target sequences" help="in the sequence database"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
239 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
240 </section> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
241 </inputs> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
242 <outputs> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
243 <data format="tabular" name="outfile" label="cmscan on ${on_string}"/> |
|
19
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
244 |
|
16
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
245 </outputs> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
246 <tests> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
247 <test> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
248 <conditional name="cm_opts"> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
249 <param name="cm_opts_selector" value="histdb"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
250 <param name="cmfile" value="minifam.cm" /> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
251 </conditional> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
252 <param name="aux_files" value="minifam.tar" ftype="tar"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
253 <param name="seqdb" value="metag-example.fa"/> |
|
19
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
254 <output name="outfile" file="test_cmscan.tabular" ftype="tabular" lines_diff="8"> |
|
16
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
255 <assert_contents> |
|
19
94cc7ef25867
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
bgruening
parents:
16
diff
changeset
|
256 <has_n_lines n="15"/> |
|
16
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
257 <has_text text="AAGA01015927.1"/> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
258 </assert_contents> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
259 </output> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
260 </test> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
261 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
262 </tests> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
263 <help> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
264 <![CDATA[ |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
265 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
266 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
267 **What it does** |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
268 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
269 cmscan is used to search sequences against collections of covariance models. |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
270 For each sequence in <seqfile>, use that query sequence to search the target database of CMs in <cmdb>, |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
271 and output ranked lists of the CMs with the most significant matches to the sequence |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
272 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
273 **Input format** |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
274 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
275 The <seqfile> may contain more than one query sequence. It can be in FASTA format, or several other common |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
276 sequence file formats (genbank, embl, and among others), or in alignment file formats (stockholm, aligned fasta, and |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
277 others). |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
278 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
279 The <cmdb> needs to be press’ed using cmpress before it can be searched with cmscan. This creates four binary |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
280 files, suffixed .i1{fimp}. Additionally, <cmdb> must have been calibrated for E-values with cmcalibrate before being |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
281 press’ed with cmpress. |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
282 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
283 NOTE: Please provid a tar file that contains the .cm file in addition to the four binary files, suffixed .i1{fimp}, |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
284 and specify the file type as "tar" before uploading the file. Otherwise Galaxy will not read the binary files properly. |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
285 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
286 **Output format** |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
287 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
288 The output format is designed to be human-readable. |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
289 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
290 For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_. |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
291 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
292 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
293 ]]> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
294 </help> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
295 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
296 <expand macro="citations" /> |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
297 |
|
0ac29b4bb1cb
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86
bgruening
parents:
diff
changeset
|
298 </tool> |