| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/presto_assemblepairs/presto_assemblepairs/0.6.2+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/presto_assemblepairs/presto_assemblepairs/0.6.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/presto_assemblepairs/presto_assemblepairs/0.5.4 |
| presto_assemblepairs |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| presto | 0.6.2 | package |
| Additional information about this tool |
ln -s '$r1_in' r1.fastq &&
ln -s '$r2_in' r2.fastq &&
#if $varExists('cc.r')
ln -s '$cc.r' reference.fasta &&
#end if
AssemblePairs.py $cc.command
--nproc "\${GALAXY_SLOTS:-1}"
-1 r1.fastq
-2 r2.fastq
--coord $coord
#if $rc
--rc '$rc'
#end if
#if $r1_annotations
--1f $r1_annotations
#end if
#if $r2_annotations
--2f $r2_annotations
#end if
#if $cc.command == "join"
--gap '$cc.gap'
#end if
#if $cc.command == "align" or $cc.command == "sequential"
--alpha '$cc.alpha'
--maxerror '$cc.maxerror'
--minlen '$cc.minlen'
--maxlen '$cc.maxlen'
$cc.scanrev
#end if
#if $cc.command == "reference" or $cc.command == "sequential"
-r reference.fasta
--minident '$cc.minident'
--evalue '$cc.evalue'
--maxhits '$cc.maxhits'
--aligner '$cc.aligner'
$cc.fill
#end if
--outdir=.
--outname=tmp
#if $capture_log
--log '$log_out'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
r1_in: presto_assemblepairs_test_r1_in.fastq r2_in: presto_assemblepairs_test_r2_in.fastq rc: tail r1_annotations: CONSCOUNT r2_annotations: PRCONS CONSCOUNT cc|gap: 10 cc|command: join coord: presto |
name: value |
presto_assemblepairs_test_r1_in.fastq presto_assemblepairs_test_r2_in.fastq value |
| Test-2 |
r1_in: presto_assemblepairs_test_r1_in.fastq r2_in: presto_assemblepairs_test_r2_in.fastq rc: tail r1_annotations: CONSCOUNT r2_annotations: PRCONS CONSCOUNT cc|scanrev: True cc|command: align coord: presto |
name: value |
presto_assemblepairs_test_r1_in.fastq presto_assemblepairs_test_r2_in.fastq value |
| Test-3 |
r1_in: presto_assemblepairs_test_r1_in.fastq r2_in: presto_assemblepairs_test_r2_in.fastq rc: tail r1_annotations: CONSCOUNT r2_annotations: PRCONS CONSCOUNT cc|r: reference_repertoire.fasta cc|aligner: blastn cc|command: reference coord: presto |
name: value |
presto_assemblepairs_test_r1_in.fastq presto_assemblepairs_test_r2_in.fastq reference_repertoire.fasta value |
| Test-4 |
r1_in: presto_assemblepairs_test_r1_in.fastq r2_in: presto_assemblepairs_test_r2_in.fastq rc: tail r1_annotations: CONSCOUNT r2_annotations: PRCONS CONSCOUNT cc|scanrev: True cc|r: reference_repertoire.fasta cc|aligner: blastn cc|command: sequential coord: presto |
name: value |
presto_assemblepairs_test_r1_in.fastq presto_assemblepairs_test_r2_in.fastq reference_repertoire.fasta value |