Repository revision
10:4f9c4e6566e5

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

Kallisto quant tool metadata
Miscellaneous
Kallisto quant
quantify abundances of RNA-Seq transcripts
kallisto_quant
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1
0.48.0+galaxy1
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy1 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.48.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.2+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.46.0.4
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.4
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.2
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.1
toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.0
kallisto_quant
Requirements (dependencies defined in the <requirements> tag set)
name version type
kallisto 0.48.0 package
samtools 1.14 package
Additional information about this tool
#if $reference_transcriptome.reference_transcriptome_source == "history":
            ln -s '$reference_transcriptome.reference' reference.fa &&
            kallisto index reference.fa -i reference.kallisto &&
            #set index_path = 'reference.kallisto'
        #else:
            #set index_path = $reference_transcriptome.index.fields.path
        #end if
        kallisto quant -i '$index_path'
            $bias --bootstrap-samples $bootstrap_samples --seed $seed $fusion  $pseudobam
            #if $pseudobam:
                -o .
            #else:
                --threads \${GALAXY_SLOTS:-1}
                -o .
            #end if
            #if str($single_paired.single_paired_selector) == 'single':
                --single
                #set $single_reads = $single_paired.reads
                --fragment-length $single_paired.fragment_length
                --sd $single_paired.sd
                '$single_reads'
            #else:
                $single_paired.lib_type
                #if str($single_paired.single_paired_selector) == 'paired_single':
                    #set $forward_reads = $single_paired.forward
                    #set $reverse_reads = $single_paired.reverse
                #else:
                    #set $forward_reads = $single_paired.reads.forward
                    #set $reverse_reads = $single_paired.reads.reverse
                #end if
                #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads)
                $reads
            #end if
            $single_overhang
            #if $genomebam_option.selector
                $genomebam_option.selector
                --gtf $genomebam_option.gtf
                --chromosomes $genomebam_option.chromosomes
            #end if
            #if $pseudobam:
                && samtools sort --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$pseudobam_output' pseudoalignments.bam
            #end if
            && cat run_info.json
None
False
Functional tests
name inputs outputs required files
Test-1 reference_transcriptome|reference: mm10_chrM.fa
reference_transcriptome|reference_transcriptome_source: history
single_paired|forward: mm10_chrM-1.f.fq
single_paired|reverse: mm10_chrM-1.r.fq
single_paired|single_paired_selector: paired_single
 name: value
 mm10_chrM.fa
mm10_chrM-1.f.fq
mm10_chrM-1.r.fq
value
Test-2 reference_transcriptome|reference: mm10_chrM.fa
reference_transcriptome|reference_transcriptome_source: history
single_paired|forward: mm10_chrM-1.f.fq
single_paired|reverse: mm10_chrM-1.r.fq
single_paired|lib_type: --fr-stranded
single_paired|single_paired_selector: paired_single
 name: value
 mm10_chrM.fa
mm10_chrM-1.f.fq
mm10_chrM-1.r.fq
value
Test-3 reference_transcriptome|reference: mm10_chrM.fa
reference_transcriptome|reference_transcriptome_source: history
single_paired|reads: paired collection
single_paired|single_paired_selector: paired_collection
 name: value
 mm10_chrM.fa
mm10_chrM-1.f.fq
mm10_chrM-1.r.fq
value
Test-4 reference_transcriptome|reference: mm10_chrM.fa
reference_transcriptome|reference_transcriptome_source: history
single_paired|reads: mm10_chrM-1.f.fq
single_paired|single_paired_selector: single
 name: value
 mm10_chrM.fa
mm10_chrM-1.f.fq
value
Test-5 reference_transcriptome|reference: felCat8_chrM.fa
reference_transcriptome|reference_transcriptome_source: history
single_paired|forward: felCat8_chrM_F.fq
single_paired|reverse: felCat8_chrM_R.fq
single_paired|single_paired_selector: paired_single
pseudobam: True
 name: value
name: value
 felCat8_chrM.fa
felCat8_chrM_F.fq
felCat8_chrM_R.fq
value
Test-6 single_paired|forward: sacCer2_chrM_F.fq.gz
single_paired|reverse: sacCer2_chrM_R.fq
single_paired|single_paired_selector: paired_single
pseudobam: True
 name: value
name: value
 sacCer2_chrM_F.fq.gz
sacCer2_chrM_R.fq
value
Test-7 reference_transcriptome|reference: hg38_transcripts.fa
reference_transcriptome|reference_transcriptome_source: history
single_paired|forward: hg38_F.fq.gz
single_paired|reverse: hg38_R.fq.gz
single_paired|single_paired_selector: paired_single
fusion: True
 name: value
 hg38_transcripts.fa
hg38_F.fq.gz
hg38_R.fq.gz
value
Test-8 reference_transcriptome|reference: transcripts.fasta
reference_transcriptome|reference_transcriptome_source: history
single_paired|forward: reads_forward.fastq.gz
single_paired|reverse: reads_reverse.fastq.gz
single_paired|single_paired_selector: paired_single
genomebam_option|gtf: annotation.gtf.gz
genomebam_option|chromosomes: chromosome_size.tabular
genomebam_option|selector: --genomebam
 name: value
 transcripts.fasta
reads_forward.fastq.gz
reads_reverse.fastq.gz
annotation.gtf.gz
chromosome_size.tabular
value