| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.30 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.3+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.4.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.3.7+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.3.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.3.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.3.3+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.3.1+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.2.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.1.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.1.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.1.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.0.4+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.0.3+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/chira_map/chira_map/1.0.2+galaxy0 |
| chira_map |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| chira | 1.4.3 | package |
| Additional information about this tool |
chira_map.py -b
-a '$alignment.aligner'
-i '$query'
#if str($alignment.aligner) == "bwa":
-s '$alignment.stranded'
-l1 '$alignment.seed_length1'
-l2 '$alignment.seed_length2'
-s1 '$alignment.align_score1'
-s2 '$alignment.align_score2'
-ma1 '$alignment.match1'
-mm1 '$alignment.mismatch1'
-ma2 '$alignment.match2'
-mm2 '$alignment.mismatch2'
-go1 '$alignment.gapo1'
-ge1 '$alignment.gape1'
-go2 '$alignment.gapo2'
-ge2 '$alignment.gape2'
-h1 '$alignment.nhits1'
-h2 '$alignment.nhits2'
#else if str($alignment.aligner) == "clan":
-s2 '$alignment.align_score'
-co '$alignment.chimeric_overlap'
#end if
#if str($reference.ref_type) == "single":
-f1 '$reference.ref_fasta'
#else if str($reference.ref_type) == "split":
-f1 '$reference.ref_fasta1'
-f2 '$reference.ref_fasta2'
#end if
-p "\${GALAXY_SLOTS:-4}"
-o ./
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
query: reads.fasta reference|ref_fasta1: ref1.fasta reference|ref_fasta2: ref2.fasta reference|ref_type: split alignment|seed_length1: 12 alignment|seed_length2: 6 alignment|align_score1: 18 alignment|align_score2: 10 alignment|aligner: bwa |
name: value name: value |
reads.fasta ref1.fasta ref2.fasta value |
| Test-2 |
query: reads.fasta reference|ref_fasta1: ref1.fasta reference|ref_fasta2: ref2.fasta reference|ref_type: split alignment|aligner: clan |
name: value |
reads.fasta ref1.fasta ref2.fasta value |