Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0 (this tool) |
cite_seq_count |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
cite-seq-count | 1.4.4 | package |
python | 3.7.12 | package |
umi_tools | 1.0.0 | package |
python-levenshtein | 0.20.7 | package |
levenshtein | 0.20.7 | package |
pandas | 0.25.3 | package |
bzip2 | 1.0.8 | package |
expat | 2.5.0 | package |
multiprocess | 0.70.14 | package |
numpy | 1.21.6 | package |
pysam | 0.16 | package |
scipy | 1.7.3 | package |
Additional information about this tool |
## This is taken from the star solo wrapper: ## Check that the input pairs are of the same type. ## We consume either repeats of two inputs R1 + R2 ## or a collection of paired reads. #if str($input_types.use) == "repeat": #assert len(str($input_types.input1).split(",")) == len(str($input_types.input2).split(",")) #set $reads1 = $input_types.input1 #set $reads2 = $input_types.input2 #elif str($input_types.use) == "list_paired": #set $reads1 = $input_types.input_collection.forward #set $reads2 = $input_types.input_collection.reverse #end if CITE-seq-Count --threads \${GALAXY_SLOTS:-4} --read1 '$reads1' --read2 '$reads2' --tags '$tags' ## Chemistry: #if str($params.chemistry) == "v2": --cell_barcode_first_base 1 --cell_barcode_last_base 16 --umi_first_base 17 --umi_last_base 26 #else if str($params.chemistry) == "v3": --cell_barcode_first_base 1 --cell_barcode_last_base 16 --umi_first_base 17 --umi_last_base 28 #else if str($params.chemistry) == "custom": --cell_barcode_first_base $params.cell_barcode_first_base --cell_barcode_last_base $params.cell_barcode_last_base --umi_first_base $params.umi_first_base --umi_last_base $params.umi_last_base #end if --bc_collapsing_dist $bc_collapsing_dist --umi_collapsing_dist $umi_collapsing_dist $no_umi_correction --expected_cells $expected_cells #if $whitelist: --whitelist '$whitelist' #end if --max-error $max_error #if str($start_trim) != "0": --start-trim $start_trim #end if $sliding_window $dense #if str($first_n) != "0": --first_n $first_n #end if #if str($unmapped.output) == "true": --unknown-top-tags $unknown_top_tags #end if ## Outputs are gzip && gunzip Results/read_count/barcodes.tsv.gz && gunzip Results/read_count/features.tsv.gz && gunzip Results/read_count/matrix.mtx.gz && gunzip Results/umi_count/barcodes.tsv.gz && gunzip Results/umi_count/features.tsv.gz && gunzip Results/umi_count/matrix.mtx.gz
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input_types|input1: correct_R1.fastq.gz input_types|input2: correct_R2.fastq.gz input_types|use: repeat tags: tags.csv params|chemistry: v2 expected_cells: 2 whitelist: whitelist.txt |
name: value name: value name: value name: value name: value name: value name: value |
correct_R1.fastq.gz correct_R2.fastq.gz tags.csv whitelist.txt value |
Test-2 |
input_types|input_collection: paired collection input_types|use: list_paired tags: tags.csv params|chemistry: v2 expected_cells: 2 dense: True |
name: value name: value name: value name: value name: value name: value name: value name: value |
correct_R1.fastq.gz correct_R2.fastq.gz tags.csv value |
Test-3 |
input_types|input1: correct_R1.fastq.gz input_types|input2: correct_R2.fastq.gz input_types|use: repeat tags: tags.csv params|cell_barcode_first_base: 1 params|cell_barcode_last_base: 16 params|umi_first_base: 17 params|umi_last_base: 26 params|chemistry: custom expected_cells: 2 whitelist: whitelist.txt max_error: 5 |
name: value name: value name: value name: value name: value name: value name: value |
correct_R1.fastq.gz correct_R2.fastq.gz tags.csv whitelist.txt value |
Test-4 |
input_types|input1: correct_R1.fastq.gz input_types|input2: correct_R2.fastq.gz input_types|use: repeat tags: tags.csv params|chemistry: v2 expected_cells: 2 whitelist: incompatible_whitelist.txt |
name: value name: value name: value name: value name: value name: value name: value |
correct_R1.fastq.gz correct_R2.fastq.gz tags.csv incompatible_whitelist.txt value |
Test-5 |
input_types|input1: correct_R1.fastq.gz input_types|input2: correct_R2.fastq.gz input_types|use: repeat tags: tags.csv params|chemistry: v2 umi_collapsing_dist: 5 expected_cells: 2 whitelist: whitelist.txt |
name: value name: value name: value name: value name: value name: value name: value |
correct_R1.fastq.gz correct_R2.fastq.gz tags.csv whitelist.txt value |
Test-6 |
input_types|input1: ['correct_R1.fastq.gz', 'correct_R1.fastq.gz'] input_types|input2: ['correct_R2.fastq.gz', 'correct_R2.fastq.gz'] input_types|use: repeat tags: tags.csv params|chemistry: v2 expected_cells: 2 whitelist: whitelist.txt |
name: value name: value name: value name: value name: value name: value name: value |
correct_R1.fastq.gz correct_R2.fastq.gz tags.csv whitelist.txt value |