Repository revision
0:3df3d1b51110

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

CITE-seq-Count tool metadata
Miscellaneous
Count CMO/HTO
cite_seq_count
toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0
1.4.4+galaxy0
CITE-seq-Count --version
True
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

None
False
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