Repository revision
18:258d696dbd7e

Repository 'stringtie'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/stringtie

StringTie tool metadata
Miscellaneous
StringTie
transcript assembly and quantification
stringtie
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.7
2.1.7
stringtie --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.7+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.7 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.1.1
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.6
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.4
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3.2
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3.1
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.3.3
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.2.3
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.1.0
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.0.4
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.0.3
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.0.1
toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/1.0.0
stringtie
Requirements (dependencies defined in the <requirements> tag set)
name version type
stringtie 2.1.7 package
samtools 1.13 package
Functional tests
name inputs outputs required files
Test-1 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: short_reads
name: value
stringtie_in1.bam
value
Test-2 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: short_reads
adv|fraction: 0.17
name: value
stringtie_in1.bam
value
Test-3 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: short_reads
guide|guide_source|ref_hist: stringtie_in.gtf
guide|guide_source|guide_gff_select: history
guide|use_guide: yes
name: value
stringtie_in1.bam
stringtie_in.gtf
value
Test-4 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: short_reads
guide|guide_source|ref_hist: stringtie_in.gtf
guide|guide_source|guide_gff_select: history
guide|use_guide: yes
adv|fraction: 0.17
name: value
stringtie_in1.bam
stringtie_in.gtf
value
Test-5 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: short_reads
guide|guide_source|ref_hist: stringtie_in.gtf
guide|guide_source|guide_gff_select: history
guide|special_outputs|special_outputs_select: ballgown
guide|coverage_file: True
guide|use_guide: yes
name: value
name: value
name: value
name: value
name: value
name: value
name: value
stringtie_in1.bam
stringtie_in.gtf
value
Test-6 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: short_reads
guide|guide_source|ref_hist: stringtie_in.gtf
guide|guide_source|guide_gff_select: history
guide|input_estimation: True
guide|special_outputs|clustering: True
guide|special_outputs|special_outputs_select: deseq2
guide|coverage_file: True
guide|use_guide: yes
name: value
name: value
name: value
name: value
name: value
stringtie_in1.bam
stringtie_in.gtf
value
Test-7 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: short_reads
guide|guide_source|ref_hist: stringtie_in.gtf
guide|guide_source|guide_gff_select: history
guide|use_guide: yes
adv|abundance_estimation: True
adv|fraction: 0.17
name: value
name: value
stringtie_in1.bam
stringtie_in.gtf
value
Test-8 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: short_reads
guide|guide_source|ref_hist: stringtie_in.gtf
guide|guide_source|guide_gff_select: history
guide|use_guide: yes
adv|fraction: 0.15
name: value
stringtie_in1.bam
stringtie_in.gtf
value
Test-9 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: short_reads
guide|guide_source|guide_gff_select: cached
guide|use_guide: yes
adv|fraction: 0.15
name: value
stringtie_in1.bam
value
Test-10 input_options|input_bam: stringtie_in1.bam
input_options|input_mode: long_reads
guide|guide_source|guide_gff_select: cached
guide|use_guide: yes
adv|fraction: 0.15
name: value
stringtie_in1.bam
value
Test-11 input_options|input_bam: long_reads.bam
input_options|error_splice: 30
input_options|input_mode: long_reads
guide|guide_source|guide_gff_select: cached
guide|use_guide: yes
adv|fraction: 0.15
name: value
long_reads.bam
value
Test-12 input_options|input_bam_short: short_reads.bam
input_options|input_bam_long: long_reads.bam
input_options|input_mode: mixed_reads
name: value
short_reads.bam
long_reads.bam
value