# HG changeset patch # User iuc # Date 1699302314 0 # Node ID d20066f6566efc573e04011914e95704e1175e38 # Parent db8a5a3195e70dc342f70382aa230996be3dcfb7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8 diff -r db8a5a3195e7 -r d20066f6566e hmmconvert.xml --- a/hmmconvert.xml Wed Jul 21 14:13:43 2021 +0000 +++ b/hmmconvert.xml Mon Nov 06 20:25:14 2023 +0000 @@ -1,12 +1,13 @@ - convert profile file to a HMMER format - - macros.xml - - - - convert profile file to a HMMER format + + macros.xml + + + + + + + + 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 + - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + + + - --E $E -#if str($T): - -T $T -#end if - -#if str($incE): - --incE $incE -#end if - -#if str($incT): - --incT $incT -#end if - - - + + + + + + + + $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 @@ - + - + @@ -342,16 +413,6 @@ - -$cut_ga -$cut_nc -$cut_tc - - - - - - --$mcs.model_construction_strategy_select diff -r db8a5a3195e7 -r d20066f6566e 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 20:25:14 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]