| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/hypo/hypo/1.0.3+galaxy0 (this tool) |
| hypo |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| hypo | 1.0.3 | package |
| Additional information about this tool |
#for $i, $fastq in enumerate($reads_short):
#if $fastq.ext.endswith(".gz")
#set $ext='.fastq.gz'
#else
#set $ext='.fastq'
#end if
ln -s '$fastq' 'read_$i$ext' &&
echo 'read_$i$ext' >> short_reads.txt &&
#end for
hypo
--reads-short @short_reads.txt
--draft '$draft'
--bam-sr '$bam_sr'
#if $bam_lr
--bam-lr '$bam_lr'
#end if
--coverage-short $coverage_short
--size-ref '$size_ref'
--kind-sr $kind_sr
#if $advanced_options.processing_size
--processing-size $advanced_options.processing_size
#end if
--match-sr $advanced_options.match_sr
--mismatch-sr $advanced_options.mismatch_sr
--gap-sr $advanced_options.gap_sr
--match-lr $advanced_options.match_lr
--mismatch-lr $advanced_options.mismatch_lr
--gap-lr $advanced_options.gap_lr
--ned-th $advanced_options.ned_th
--qual-map-th $advanced_options.qual_map_th
-o '$out_fasta'
-t \${GALAXY_SLOTS:-4}
#if $advanced_options.log == 'true'
> '$out_log'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reads_short: ['Illumina_01.fastq.gz', 'Illumina_02.fastq.gz'] draft: draft_genome.fasta bam_sr: short_reads.bam coverage_short: 35 size_ref: 10k |
name: value |
Illumina_01.fastq.gz Illumina_02.fastq.gz draft_genome.fasta short_reads.bam value |
| Test-2 |
reads_short: ['Illumina_01.fastq.gz', 'Illumina_02.fastq.gz'] draft: draft_genome.fasta bam_sr: short_reads.bam bam_lr: long_reads.bam coverage_short: 35 size_ref: 10k |
name: value |
Illumina_01.fastq.gz Illumina_02.fastq.gz draft_genome.fasta short_reads.bam long_reads.bam value |
| Test-3 |
reads_short: ['Illumina_01.fastq.gz', 'Illumina_02.fastq.gz'] draft: draft_genome.fasta bam_sr: short_reads.bam bam_lr: long_reads.bam coverage_short: 35 size_ref: 10k |
name: value |
Illumina_01.fastq.gz Illumina_02.fastq.gz draft_genome.fasta short_reads.bam long_reads.bam value |
| Test-4 |
reads_short: ['Illumina_01.fastq.gz', 'Illumina_02.fastq.gz'] draft: draft_genome.fasta bam_sr: short_reads.bam bam_lr: long_reads.bam coverage_short: 35 size_ref: 10k |
name: value |
Illumina_01.fastq.gz Illumina_02.fastq.gz draft_genome.fasta short_reads.bam long_reads.bam value |
| Test-5 |
reads_short: ['Illumina_01.fastq.gz', 'Illumina_02.fastq.gz'] draft: draft_genome.fasta bam_sr: short_reads.bam coverage_short: 35 size_ref: 10k advanced_options|log: True |
name: value name: value |
Illumina_01.fastq.gz Illumina_02.fastq.gz draft_genome.fasta short_reads.bam value |
| Test-6 |
reads_short: ['Illumina_01.fastq.gz', 'Illumina_02.fastq.gz'] draft: draft_genome.fasta bam_sr: short_reads.bam bam_lr: long_reads.bam coverage_short: 35 size_ref: 10k advanced_options|match_sr: 4 advanced_options|mismatch_sr: -2 advanced_options|gap_sr: -10 advanced_options|match_lr: 3 advanced_options|mismatch_lr: -7 advanced_options|gap_lr: -15 advanced_options|ned_th: 10 advanced_options|qual_map_th: 4 |
name: value |
Illumina_01.fastq.gz Illumina_02.fastq.gz draft_genome.fasta short_reads.bam long_reads.bam value |
| Test-7 |
reads_short: ['Illumina_01.fastq', 'Illumina_02.fastq'] draft: draft_genome.fasta bam_sr: short_reads.bam coverage_short: 35 size_ref: 10k |
name: value |
Illumina_01.fastq Illumina_02.fastq draft_genome.fasta short_reads.bam value |