| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/2.10.1+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/2.10.1+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/2.9.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/2.7.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.3.3 |
| toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeprofiledb/0.1.01 |
| ncbi_makeprofiledb |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| blast | 2.10.1 | package |
| Additional information about this tool |
##Unlike makeblastdb, makeprofiledb needs directory to exist already:
mkdir -p $outfile.files_path &&
makeprofiledb
-blastdb_version 4
-out '${os.path.join($outfile.files_path, "blastdb")}'
##We turn $input_file into $infiles with a configfile entry defined below
-in '$infiles'
#if $title:
-title '$title'
#else:
##Would default to being based on the cryptic Galaxy filenames, which is unhelpful
-title 'Profile Database'
#end if
-threshold $threshold
#if str($contain_pssm_scores.contain_pssm_scores_type) == 'no':
-gapopen $contain_pssm_scores.gapopen
-gapextend $contain_pssm_scores.gapextend
-scale $contain_pssm_scores.scale
-matrix $contain_pssm_scores.matrix
#end if
-obsr_threshold $obsr_threshold
-exclude_invalid $exclude_invalid
-logfile '$outfile'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_file: ['cd00003.smp', 'cd00008.smp'] title: Just 2 PSSM matrices contain_pssm_scores|contain_pssm_scores_type: yes |
name: value |
cd00003.smp cd00008.smp value |