# HG changeset patch
# User iuc
# Date 1699302402 0
# Node ID 5cbef50c0c635367b0bace9bd4536403af9d7b64
# Parent 6e27bb3f0fa6642f8309e067f467727fd40c3033
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8
diff -r 6e27bb3f0fa6 -r 5cbef50c0c63 jackhmmer.xml
--- a/jackhmmer.xml Wed Jul 21 14:16:41 2021 +0000
+++ b/jackhmmer.xml Mon Nov 06 20:26:42 2023 +0000
@@ -4,6 +4,7 @@
macros.xml
+
+
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+ hmmer3
+
+
3.3.2
@@ -17,69 +22,135 @@
+
+
--E $E
---domE $domE
-
-#if str($T):
- -T $T
-#end if
-
-#if str($domT):
- --domT $domT
+#if $repopt.repopt_sel == "evalue"
+ -E $repopt.E
+ #if str($repopt.incE) != ""
+ --incE $repopt.incE
+ #end if
+#elif $repopt.repopt_sel == "score"
+ -T $repopt.T
+ #if str($repopt.incT) != ""
+ --incT $repopt.incT
+ #end if
+#else
+ $repopt.repopt_sel
#end if
-
-#if str($incE):
- --incE $incE
-#end if
-
-#if str($incdomE):
- --incdomE $incdomE
-#end if
-
-#if str($incT):
- --incT $incT
-#end if
-
-#if str($incdomT):
- --incdomT $incdomT
+
+
+
+#if $repopt.repopt_sel == "evalue"
+ --domE $repopt.domE
+ #if str($repopt.incdomE) != ""
+ --incdomE $repopt.incdomE
+ #end if
+#elif $repopt.repopt_sel == "score"
+ --domT $repopt.domT
+ #if str($repopt.incdomT) != ""
+ --incdomT $repopt.incdomT
+ #end if
#end if
+
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-
--E $E
-#if str($T):
- -T $T
-#end if
-
-#if str($incE):
- --incE $incE
-#end if
-
-#if str($incT):
- --incT $incT
-#end if
-
-
-
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+
$max
--F1 $F1
@@ -115,7 +186,7 @@
-#if $oformat:
+#if $oformat:
#for o in str($oformat).split(','):
--$o '$getVar($o, 'MISSING_OUTPUT'+$o)'
#end for
@@ -144,7 +215,7 @@
-
+
@@ -192,14 +263,14 @@
-
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-
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@@ -342,16 +413,6 @@
-
-$cut_ga
-$cut_nc
-$cut_tc
-
-
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-
-
-
--$mcs.model_construction_strategy_select
diff -r 6e27bb3f0fa6 -r 5cbef50c0c63 test-data/cut_ga_test.out
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cut_ga_test.out Mon Nov 06 20:26:42 2023 +0000
@@ -0,0 +1,45 @@
+# hmmsearch :: search profile(s) against a sequence database
+# HMMER 3.3.2 (Nov 2020); http://hmmer.org/
+# Copyright (C) 2020 Howard Hughes Medical Institute.
+# Freely distributed under the BSD open source license.
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# query HMM file: /tmp/saskia/tmpug0qcpsy/files/9/9/b/dataset_99bcd3c6-6d16-4e09-9878-7117f928bb24.dat
+# target sequence database: /tmp/saskia/tmpug0qcpsy/files/f/9/9/dataset_f99d0a82-fcb5-4323-b2d4-8b218045c72e.dat
+# max ASCII text line length: unlimited
+# model-specific thresholding: GA cutoffs
+# Vit filter P threshold: <= 0.001
+# Fwd filter P threshold: <= 1e-05
+# random number seed set to: 4
+# number of worker threads: 0
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query: fn3 [M=86]
+Accession: PF00041.13
+Description: Fibronectin type III domain
+Scores for complete sequences (score includes all domains):
+ --- full sequence --- --- best 1 domain --- -#dom-
+ E-value score bias E-value score bias exp N Sequence Description
+ ------- ------ ----- ------- ------ ----- ---- -- -------- -----------
+
+ [No hits detected that satisfy reporting thresholds]
+
+
+Domain annotation for each sequence (and alignments):
+
+ [No targets detected that satisfy reporting thresholds]
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query model(s): 1 (86 nodes)
+Target sequences: 2 (301 residues searched)
+Passed MSV filter: 0 (0); expected 0.0 (0.02)
+Passed bias filter: 0 (0); expected 0.0 (0.02)
+Passed Vit filter: 0 (0); expected 0.0 (0.001)
+Passed Fwd filter: 0 (0); expected 0.0 (1e-05)
+Initial search space (Z): 2 [actual number of targets]
+Domain search space (domZ): 0 [number of targets reported over threshold]
+# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
+# Mc/sec: 144.45
+//
+[ok]