| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.48.0+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq_count/1.0 |
| dexseq_count |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-dexseq | 1.48.0 | package |
| r-getopt | 1.20.4 | package |
| r-rjson | 0.2.21 | package |
| Additional information about this tool |
#if $mode.mode_select == "prepare":
dexseq_prepare_annotation.py
-r '${mode.aggregate}'
'${mode.gtffile}'
'$flattened_gtf_out'
#elif $mode.mode_select == "count":
ln -s -f '${mode.bamfile}' 'input.bam' &&
ln -s -f '${mode.bamfile.metadata.bam_index}' 'input.bam.bai' &&
dexseq_count.py
--format bam
--paired '${mode.paired}'
--stranded '${mode.stranded}'
--minaqual '${mode.qual}'
--order '${mode.order}'
'${mode.flattened_gtf_in}'
'input.bam'
'$counts_file'
&&
sed -i 's/\"//g' '$counts_file'
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
mode|gtffile: original.gtf mode|aggregate: True mode|mode_select: prepare |
name: value |
original.gtf value |
| Test-2 |
mode|bamfile: in.bam mode|flattened_gtf_in: flattened.gtf mode|stranded: no mode|mode_select: count |
name: value |
in.bam flattened.gtf value |