Repository revision
8:c9e29ac5d099

Repository 'infernal'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/infernal

cmsearch tool metadata
Miscellaneous
cmsearch
Search covariance model(s) against a sequence database
infernal_cmsearch
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0
1.1.4+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.4+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/infernal/infernal_cmsearch/1.1.0.2
infernal_cmsearch
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
## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
        ## it will be converted to a tab delimited file and piped to Galaxy
        temp_tabular_output=\$(mktemp) &&

        cmsearch
            ## Infernal Options
            --cpu "\${GALAXY_SLOTS:-2}"
            -o /dev/null
            --tformat $seqdb.ext ##target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip
            $bottomonly
            $toponly
            $cyk
            $acyk
            $notrunc
            $anytrunc
            $nonull3
            #if str($smxsize) != "128.0"
                --smxsize $smxsize
            #end if
            #if str($mxsize) != "128.0"
                --mxsize $mxsize
            #end if
            --tblout \$temp_tabular_output
            $g
            #if $Z
                -Z $Z
            #end if
            #if $A:
                $A '$multiple_alignment_output'
            #end if
            #if str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incE":
                --incE $inclusion_thresholds_opts.incE
            #elif str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incT":
                --incT $inclusion_thresholds_opts.incT
            #end if
            #if str($reporting_thresholds_opts.reporting_thresholds_selector) == "-E":
                -E $reporting_thresholds_opts.E
            #elif str($reporting_thresholds_opts.reporting_thresholds_selector) == "-T":
                -T $reporting_thresholds_opts.T
            #end if
            $model_thresholds.cut_ga
            $model_thresholds.cut_nc
            $model_thresholds.cut_tc
            #if $acceleration_huristics.acceleration_huristics_selector == "FZ"
                --FZ $$acceleration_huristics.FZ
            #else
                $acceleration_huristics.acceleration_huristics_selector
                #if $acceleration_huristics.acceleration_huristics_selector == "--mid"
                    --Fmid $acceleration_huristics.Fmid
                #end if
            #end if
            ## CM file from the history or stored as database on disc
            #if str($cm_opts.cm_opts_selector) == "db":
                $cm_opts.database.fields.path
            #else:
                $cm_opts.cmfile
            #end if
            ## sequence file
            '$seqdb'
            2>&1
            &&
            ## 1. replace all lines starting # (comment lines)
            ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
            sed -e 's/#.*$//' -e '/^$/d' -e 's/\s\+/\t/g' -e 's/\t/ /18g' \$temp_tabular_output > '$outfile'


    
None
False
False
Functional tests
name inputs outputs required files
Test-1 seqdb: cmsearch_input2.fa
cm_opts|cmfile: cmsearch_input1.cm
cm_opts|cm_opts_selector: histdb
name: value
cmsearch_input2.fa
cmsearch_input1.cm
value