| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy5 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy3 |
| toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy2 |
| toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.3+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/salsa/salsa/2.2+galaxy0 |
| salsa |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| salsa2 | 2.3 | package |
| samtools | 1.11 | package |
| Additional information about this tool |
ln -s '$fasta_in' input.fasta &&
samtools faidx input.fasta &&
run_pipeline.py
-a '$fasta_in'
-l input.fasta.fai
#if $enzyme_conditional.enzyme_options == 'preconfigured':
#if $enzyme_conditional.preconfigured_enzymes == 'dovetail'
-e 'GATC'
#else if $enzyme_conditional.preconfigured_enzymes == 'arima1'
-e 'GATC,GANTC'
#else if $enzyme_conditional.preconfigured_enzymes == 'arima2'
-e 'GATC,GANTC,CTNAG,TTAA'
#else if $enzyme_conditional.preconfigured_enzymes == 'omnic'
-e 'DNASE'
#end if
#else:
-e '${enzyme_conditional.manual_enzyme}'
#end if
-b '$bed_file'
#if str($cutoff):
-c '$cutoff'
#end if
#if $gfa_file:
-g '$gfa_file'
#end if
#if $iter:
-i '$iter'
#end if
#if $gensize:
-s '$gensize'
#end if
-m '$clean'
-o ./out
&&
## The tool seems to generate malformed AGP. Print exactly
## 9 tab-delimited columns, adding blank columns or
## removing columns if necessary.
awk -F'\t'
'{while(NF<9)\$0=\$0 FS""; if(NF>9)\$9=\$9 FS \$(NF--); print \$1,\$2,\$3,\$4,\$5,\$6,\$7,\$8,\$9}'
OFS='\t' out/scaffolds_FINAL.agp
| cut -f1-9
> out/scaffolds_FINAL.fixed.agp
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fasta_in: test.fasta bed_file: test.bed cutoff: 1000 gfa_file: test.gfa1 enzyme_conditional|manual_enzyme: GATC,GANTC enzyme_conditional|enzyme_options: specific iter: 3 clean: True |
name: value name: value |
test.fasta test.bed test.gfa1 value |
| Test-2 |
fasta_in: test.fasta bed_file: test.bed cutoff: 1000 gfa_file: test.gfa1 enzyme_conditional|preconfigured_enzymes: arima1 enzyme_conditional|enzyme_options: preconfigured iter: 3 clean: True |
name: value name: value |
test.fasta test.bed test.gfa1 value |
| Test-3 |
fasta_in: test.fasta bed_file: test.bed cutoff: 1000 gfa_file: test.gfa1 enzyme_conditional|preconfigured_enzymes: arima1 enzyme_conditional|enzyme_options: preconfigured iter: 3 clean: True |
name: value name: value |
test.fasta test.bed test.gfa1 value |