| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/optitype/optitype/1.3.5+galaxy0 (this tool) |
| optitype |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| optitype | 1.3.5 | package |
| Additional information about this tool |
export MPLCONFIGDIR=\$TEMP &&
#set $fastqs = []
#if str( $fastq_input.fastq_input_selector ) == "paired":
ln -s '${fastq_input.fastq_input1}' reads_1.fastq
&& ln -s '${fastq_input.fastq_input2}' reads_2.fastq
#set $fastqs = ['reads_1.fastq','reads_2.fastq']
#elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
ln -s '${fastq_input.fastq_input1.forward}' reads_1.fastq
&& ln -s '${fastq_input.fastq_input1.reverse}' reads_2.fastq
#set $fastqs = ['reads_1.fastq','reads_2.fastq']
#elif str( $fastq_input.fastq_input_selector ) == "single":
ln -s '${fastq_input.fastq_input1}' reads.fastq
#set $fastqs = ['reads.fastq']
#end if
&& RAZERS3=`which razers3`
&& sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\${GALAXY_SLOTS}/" > config.ini
#set $input_fq = ' '.join($fastqs)
&& OptiTypePipeline.py
$read_type --input ${' '.join($fastqs)}
#if str($beta) != '':
--beta $beta
#end if
#if str($enumerations) != '':
--enumerate $enumerations
#end if
--config "`pwd`/config.ini"
--outdir outdir
&& cp outdir/*/*_coverage_plot.pdf '$coverage_plot'
&& cp outdir/*/*_result.tsv '$result'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fastq_input|fastq_input1: rna/CRC_81_N_1_fished.fastq fastq_input|fastq_input2: rna/CRC_81_N_2_fished.fastq fastq_input|fastq_input_selector: paired read_type: --rna solver: glpk |
name: value |
rna/CRC_81_N_1_fished.fastq rna/CRC_81_N_2_fished.fastq value |
| Test-2 |
fastq_input|fastq_input1: exome/NA11995_SRR766010_1_fished.fastq fastq_input|fastq_input2: exome/NA11995_SRR766010_2_fished.fastq fastq_input|fastq_input_selector: paired read_type: --dna enumerations: 2 solver: glpk unpaired_weight: 0.2 |
name: value |
exome/NA11995_SRR766010_1_fished.fastq exome/NA11995_SRR766010_2_fished.fastq value |