| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mash_sketch/mash_sketch/2.3+galaxy0 (this tool) |
| mash_sketch |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| mash | 2.3 | package |
| Additional information about this tool |
mash sketch
-s '${sketch_size}'
-k '${kmer_size}'
-w '${prob_threshold}'
#if str ( $reads_assembly.reads_assembly_selector ) == "reads"
-m '${reads_assembly.minimum_kmer_copies}'
-r
#if $reads_assembly.target_coverage
-c '${reads_assembly.target_coverage}'
#end if
#if $reads_assembly.genome_size
-g '${reads_assembly.genome_size}'
#end if
#if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"
'$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2'
#end if
#if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection"
'$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse'
#end if
#if str( $reads_assembly.reads_input.reads_input_selector ) == "single"
'$reads_assembly.reads_input.reads'
#end if
#elif str ( $reads_assembly.reads_assembly_selector ) == "assembly"
-p \${GALAXY_SLOTS:-1}
'${assembly}'
${reads_assembly.individual_sequences}
#end if
-o 'sketch'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reads_assembly|reads_input|reads: ERR024951_seqtk_sample_1000_1.fastq reads_assembly|reads_input|reads_input_selector: single reads_assembly|reads_assembly_selector: reads |
name: value |
ERR024951_seqtk_sample_1000_1.fastq value |
| Test-2 |
reads_assembly|reads_input|reads: ERR024951_seqtk_sample_1000_1.fastq reads_assembly|reads_input|reads_input_selector: single reads_assembly|reads_assembly_selector: reads |
name: value |
ERR024951_seqtk_sample_1000_1.fastq value |
| Test-3 |
reads_assembly|reads_input|reads: ERR024951_seqtk_sample_1000_1.fastq reads_assembly|reads_input|reads_input_selector: single reads_assembly|reads_assembly_selector: reads |
name: value |
ERR024951_seqtk_sample_1000_1.fastq value |
| Test-4 |
reads_assembly|reads_input|reads: ERR024951_seqtk_sample_1000_1.fastq reads_assembly|reads_input|reads_input_selector: single reads_assembly|reads_assembly_selector: reads |
name: value |
ERR024951_seqtk_sample_1000_1.fastq value |
| Test-5 |
reads_assembly|reads_input|reads: ERR024951_seqtk_sample_1000_1.fastq reads_assembly|reads_input|reads_input_selector: single reads_assembly|reads_assembly_selector: reads sketch_size: 500 |
name: value |
ERR024951_seqtk_sample_1000_1.fastq value |
| Test-6 |
reads_assembly|reads_input|reads: ERR024951_seqtk_sample_1000_1.fastq reads_assembly|reads_input|reads_input_selector: single reads_assembly|reads_assembly_selector: reads kmer_size: 17 |
name: value |
ERR024951_seqtk_sample_1000_1.fastq value |
| Test-7 |
reads_assembly|reads_input|reads: ERR024951_seqtk_sample_1000_1.fastq reads_assembly|reads_input|reads_input_selector: single reads_assembly|reads_assembly_selector: reads prob_threshold: 0.1 |
name: value |
ERR024951_seqtk_sample_1000_1.fastq value |
| Test-8 |
reads_assembly|assembly: test_assembly.fasta reads_assembly|reads_assembly_selector: assembly |
name: value |
test_assembly.fasta value |