| 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/1.1.6+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/1.1.5+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/1.1.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_whitelist/umi_tools_whitelist/1.1.2+galaxy2 |
| 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 | 1.1.6 | package |
| samtools | 1.21 | package |
| sed | 4.7 | 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 |