Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/1.1.2+galaxy2 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/1.1.2+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/1.1.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/0.5.5.0 |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/0.5.3.1 |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/0.5.3.0 |
umi_tools_whitelist |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
umi_tools | 1.1.2 | package |
Additional information about this tool |
#import json #set $gz = False #if $input_type_cond.input_type == 'single': #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"): ln -s '$input_type_cond.input_read1' input_single.gz && #set $gz = True #else ln -s '$input_type_cond.input_read1' input_single.txt && #end if #elif $input_type_cond.input_type == 'paired': #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"): ln -s '$input_type_cond.input_read1' input_read1.gz && ln -s '$input_type_cond.input_read2' input_read2.gz && #set $gz = True #else ln -s '$input_type_cond.input_read1' input_read1.txt && ln -s '$input_type_cond.input_read2' input_read2.txt && #end if #else ## paired_collection #if $input_type_cond.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"): ln -s '$input_type_cond.input_readpair.forward' input_read1.gz && ln -s '$input_type_cond.input_readpair.reverse' input_read2.gz && #set $gz = True #else ln -s '$input_type_cond.input_readpair.forward' input_read1.txt && ln -s '$input_type_cond.input_readpair.reverse' input_read2.txt && #end if #end if umi_tools whitelist ## fastq barcode extraction options: --extract-method='$extract_method_cond.extract_method' --bc-pattern='$input_type_cond.bc_pattern' #if $input_type_cond.input_type != 'single' and $input_type_cond.bc_pattern2 != '' --bc-pattern2='$input_type_cond.bc_pattern2' #end if #if $extract_method_cond.extract_method == 'string' $extract_method_cond.prime3 #else if $extract_method_cond.filtered_out_bool #if $input_type_cond.input_type == 'single': --filtered-out='$filtered_out' #else if $input_type_cond.input_type == 'paired': --filtered-out='$filtered_out' --filtered-out2='$filtered_out_paired' #else --filtered-out='$filtered_out_paired_collection.forward' --filtered-out2='$filtered_out_paired_collection.reverse' #end if #end if $ignore_read_pair_suffixes --subset-reads='$subset_reads' $allow_threshold_error #if $ed_above_threshold --ed-above-threshold=$ed_above_threshold #end if --knee-method='$knee_method' #if $input_type_cond.input_type == 'single': #if $gz: --stdin=input_single.gz #else --stdin=input_single.txt #end if #else: ## equally valid for both 'paired' and 'paired_collection' #if $gz: --stdin=input_read1.gz --read2-in=input_read2.gz #else: --stdin=input_read1.txt --read2-in=input_read2.txt #end if #end if #if $celloptions.use_cell_opts == "advanced": #if str($celloptions.set_cell_number) != '': --set-cell-number=$celloptions.set_cell_number #end if #if str($celloptions.expect_cells) != '': --expect-cells=$celloptions.expect_cells #end if --error-correct-threshold=$celloptions.error_correct_threshold #end if --method=$method --plot-prefix=OUT #if $log: --log='$out_log' #end if --log2stderr > '$out_whitelist' && mkdir '${ out_html_report.files_path }' && cp OUT_*.png '${ out_html_report.files_path }' && echo "<html> <head></head><body> <h1>Cell and Count Metrics</h1> <img src=\"OUT_cell_barcode_count_density.png\" ><br /> <img src=\"OUT_cell_barcode_knee.png\" ><br /> <img src=\"OUT_cell_barcode_counts.png\" ><br /> </body></html>" > '$out_html_report' && mv OUT_cell_thresholds.tsv '$out_thresh'
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input_type_cond|input_read1: t_R2.fastq.gz input_type_cond|bc_pattern: CCCCCCCCNNNNNNNN input_type_cond|input_type: single extract_method_cond|prime3: True method: reads knee_method: density |
name: value name: value name: value |
t_R2.fastq.gz value |
Test-2 |
input_type_cond|input_read1: t_R1.fastq.gz input_type_cond|input_read2: t_R2.fastq.gz input_type_cond|bc_pattern: CCCNNNNNNNNXXXXX input_type_cond|input_type: paired extract_method_cond|prime3: False method: reads knee_method: density celloptions|expect_cells: 5 celloptions|error_correct_threshold: 3 celloptions|use_cell_opts: advanced log: True |
name: value name: value name: value name: value |
t_R1.fastq.gz t_R2.fastq.gz value |
Test-3 |
input_type_cond|input_readpair: paired collection input_type_cond|bc_pattern: CCCNNNNNNNNXXXXX input_type_cond|input_type: paired_collection extract_method_cond|prime3: False method: reads knee_method: density celloptions|expect_cells: 5 celloptions|error_correct_threshold: 3 celloptions|use_cell_opts: advanced log: True |
name: value name: value name: value name: value |
t_R1.fastq.gz t_R2.fastq.gz value |
Test-4 |
input_type_cond|input_read1: testYYY.40k.fastq.gz input_type_cond|bc_pattern: (?P<cell_1>.{8,10})(?P<discard_1>ACTGGCCTGCGA){s<=3}(?P<cell_2>.{9})(?P<discard_2>GGTAGCGGTGACA){s<=3}(?P<cell_3>.{9})(?P<umi_1>.{8})T{3}.* input_type_cond|input_type: single extract_method_cond|filtered_out_bool: True extract_method_cond|extract_method: regex method: umis knee_method: density |
name: value name: value name: value name: value |
testYYY.40k.fastq.gz value |