Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.4+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmbuild/1.1.0.1 |
infernal_cmbuild |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
infernal | not provided | package |
infernal | 1.1.4 | package |
coreutils | 8.32 | package |
Additional information about this tool |
cmbuild -F #if $is_summery_output: -o '$summary_outfile' #end if ## to many outputs, is that one really needed? ##-O $annotated_source_alignment_outfile $model_construction_opts.model_construction_opts_selector #if $model_construction_opts.model_construction_opts_selector == '--fast': --symfrac $model_construction_opts.symfrac #end if $noss $relative_weights_opts.relative_weights_opts_selector #if $relative_weights_opts.relative_weights_opts_selector == '--wblosum': --wid $relative_weights_opts.wid #end if --p7ere $controlling_filter_p7_hmm.p7ere $controlling_filter_p7_hmm.p7ml --EmN $controlling_filter_p7_hmm.EmN --EvN $controlling_filter_p7_hmm.EvN --ElfN $controlling_filter_p7_hmm.ElfN --EgfN $controlling_filter_p7_hmm.EgfN $effective_opts.effective_opts_selector #if str($effective_opts.effective_opts_selector) == '--eent': #if $effective_opts.ere --ere $effective_opts.ere #end if #if $effective_opts.eminseq --eminseq $effective_opts.eminseq #end if #if $effective_opts.emaxseq --emaxseq $effective_opts.emaxseq #end if #if $effective_opts.ehmmre --ehmmre $effective_opts.ehmmre #end if #if $effective_opts.eset --eset $effective_opts.eset #end if #end if #if str($refining_opts.refining_opts_selector) == '--refine': #if $refining_opts.refine_output: --refine '$refined_multiple_alignment_output' #else: --refine /dev/null #end if $refining_opts.l $refining_opts.gibbs_opts.gibbs_opts_selector #if str($refining_opts.gibbs_opts.gibbs_opts_selector) == '--gibbs': --seed $refining_opts.gibbs_opts.random_seed #end if $refining_opts.notrunc $refining_opts.cyk #end if '$cmfile_outfile' '$alignment_infile' #if $Calibrate.selector=="true" && cmcalibrate -L $Calibrate.L #if $Calibrate.output_options_cond.selector == "extra" #if str($Calibrate.output_options_cond.output_options) != 'None' #for j in $Calibrate.output_options_cond.output_options.value: --$j $getVar($j) #end for #end if #end if #if $Calibrate.cont_exp_tails_fits.selector == "top_n" --gtailn $Calibrate.cont_exp_tails_fits.gtailn --ltailn $Calibrate.cont_exp_tails_fits.ltailn #elif $Calibrate.cont_exp_tails_fits.selector == "frac" --tailp $Calibrate.cont_exp_tails_fits.tailp #end if --seed $Calibrate.add_opts.seed --beta $Calibrate.add_opts.beta $Calibrate.add_opts.nonbanded $Calibrate.add_opts.nonull3 $Calibrate.add_opts.random #if str($Calibrate.add_opts.gc) != 'None' --gc '$Calibrate.add_opts.gc' #end if --cpu "\${GALAXY_SLOTS:-2}" '$cmfile_outfile' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
alignment_infile: cmbuild_input_tRNA5.sto Calibrate|L: 0.1 Calibrate|selector: True |
name: value |
cmbuild_input_tRNA5.sto value |
Test-2 |
alignment_infile: cmbuild_input_tRNA5.sto effective_opts|emaxseq: 100 effective_opts|effective_opts_selector: --eent Calibrate|L: 0.1 Calibrate|selector: True |
name: value |
cmbuild_input_tRNA5.sto value |