Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/3.4+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/3.3.2+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/3.3.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/3.3+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/3.3 |
toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/3.2 |
toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/3.1b2 |
toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/0.1.1 |
toolshed.g2.bx.psu.edu/repos/iuc/hmmer_hmmscan/hmmer_hmmscan/0.1.0 |
hmmer_hmmscan |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
hmmer | 3.4 | package |
Additional information about this tool |
##compute the number of ADDITIONAL threads to be used (--cpu) addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && #if $input_hmm_conditional.input_hmm_source == "history": #set $input_hmm_filename = "localref.hmm" ln -s '${input_hmm_conditional.hmmfile}' '${input_hmm_filename}' && ## "Press" database hmmpress '${input_hmm_filename}' && #else: #set $input_hmm_filename = str($input_hmm_conditional.index.fields.db_path) #end if hmmscan #if $oformat: #for o in str($oformat).split(','): --$o '$getVar($o, 'MISSING_OUTPUT'+$o)' #end for #end if $acc $noali $notextw #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 $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 $max --F1 $F1 --F2 $F2 --F3 $F3 $nobias $nonull2 #if str($Z): -Z $Z #end if #if str($domZ): --domZ $domZ #end if --cpu \$addthreads --seed $seed '$input_hmm_filename' '$seqfile' > '$output'
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input_hmm_conditional|hmmfile: MADE1.hmm input_hmm_conditional|input_hmm_source: history seqfile: dna_target2.fa notextw: True seed: 4 |
name: value name: value name: value name: value |
MADE1.hmm dna_target2.fa value |