| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.48.0+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.2+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.2 |
| toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.46.0.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.43.1.1 |
| toolshed.g2.bx.psu.edu/repos/iuc/kallisto_pseudo/kallisto_pseudo/0.43.1.0 |
| kallisto_pseudo |
| 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 = $reference_transcriptome.index.fields.path
#end if
kallisto pseudo -i '$index_path'
--threads \${GALAXY_SLOTS:-1}
-o .
#if str($single_paired.single_paired_selector) == 'single':
--single --fragment-length $single_paired.fragment_length
--sd $single_paired.sd '$single_paired.reads'
#else:
#if str($single_paired.collection.collection_selector) == 'collection':
'$single_paired.collection.reads.forward'
'$single_paired.collection.reads.reverse'
#else:
#if str($single_paired.collection.fastq_umi.umi) == 'yes':
--batch '$batch' --umi
#else:
'$single_paired.collection.fastq_umi.forward'
'$single_paired.collection.fastq_umi.reverse'
#end if
#end if
#end if
&& if [ -f run_info.json ] ; then cat run_info.json ; fi &&
mkdir outputs &&
if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi &&
if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi &&
if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi &&
if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi &&
if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
reference_transcriptome|reference: mm10_chrM.fa reference_transcriptome|reference_transcriptome_source: history single_paired|collection|fastq_umi|forward: mm10_chrM.umi single_paired|collection|fastq_umi|reverse: mm10_chrM-1.r.fq.gz single_paired|collection|fastq_umi|umi: yes single_paired|collection|collection_selector: datasets single_paired|single_paired_selector: paired |
name: value |
mm10_chrM.fa mm10_chrM.umi mm10_chrM-1.r.fq.gz value |
| Test-2 |
reference_transcriptome|reference: mm10_chrM.fa reference_transcriptome|reference_transcriptome_source: history single_paired|collection|reads: paired collection single_paired|collection|collection_selector: collection single_paired|single_paired_selector: paired |
name: value |
mm10_chrM.fa mm10_chrM-1.f.fq.gz mm10_chrM-1.r.fq.gz value |
| Test-3 |
reference_transcriptome|reference: mm10_chrM.fa reference_transcriptome|reference_transcriptome_source: history single_paired|reads: mm10_chrM-1.f.fq.gz single_paired|single_paired_selector: single |
name: value |
mm10_chrM.fa mm10_chrM-1.f.fq.gz value |
| Test-4 |
reference_transcriptome|reference: felCat8_chrM.fa reference_transcriptome|reference_transcriptome_source: history single_paired|collection|fastq_umi|forward: felCat8_chrM_F.fq single_paired|collection|fastq_umi|reverse: felCat8_chrM_R.fq single_paired|collection|fastq_umi|umi: no single_paired|collection|collection_selector: datasets single_paired|single_paired_selector: paired |
name: value |
felCat8_chrM.fa felCat8_chrM_F.fq felCat8_chrM_R.fq value |
| Test-5 |
single_paired|collection|fastq_umi|forward: sacCer2_chrM.umi single_paired|collection|fastq_umi|reverse: sacCer2_chrM_R.fq.gz single_paired|collection|fastq_umi|umi: yes single_paired|collection|collection_selector: datasets single_paired|single_paired_selector: paired |
name: value |
sacCer2_chrM.umi sacCer2_chrM_R.fq.gz value |