Mercurial > repos > iuc > umi_tools_whitelist
annotate umi-tools_whitelist.xml @ 0:b911124762a8 draft
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
author | iuc |
---|---|
date | Sun, 25 Feb 2018 13:07:58 -0500 |
parents | |
children | dac4e7dc837d |
rev | line source |
---|---|
0
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
1 <tool id="umi_tools_whitelist" name="UMI-tools whitelist" version="@VERSION@.0"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
2 <description>Extract cell barcodes from FASTQ files</description> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
3 <macros> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
5 </macros> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
6 <expand macro="requirements" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
7 <command detect_errors="exit_code"><![CDATA[ |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
8 #set $gz = False |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
9 #if $input_type.type == 'single': |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
10 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"): |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
11 ln -s '$input_type.input_single' input_single.gz && |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
12 #set $gz = True |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
13 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
14 #else |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
15 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"): |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
16 ln -s '$input_type.input_read1' input_read1.gz && |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
17 ln -s '$input_type.input_read2' input_read2.gz && |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
18 #set $gz = True |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
19 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
20 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
21 umi_tools whitelist |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
22 --bc-pattern='$bc_pattern' |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
23 --subset-reads='$subset_reads' |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
24 #if $input_type.type == 'single': |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
25 #if $gz: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
26 --stdin=input_single.gz |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
27 #else |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
28 --stdin='$input_type.input_single' |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
29 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
30 #else: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
31 #if $gz: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
32 --stdin=input_read1.gz |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
33 --read2-in=input_read2.gz |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
34 #else: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
35 --stdin='$input_type.input_read1' |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
36 --read2-in='$input_type.input_read2' |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
37 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
38 #if $input_type.barcode.barcode_select == "1": |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
39 --bc-pattern2='$input_type.barcode.bc_pattern2' |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
40 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
41 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
42 #if $celloptions.use_cell_opts == "advanced": |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
43 #if $celloptions.set_cell_number != "0": |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
44 --set-cell-number=$celloptions.set_cell_number |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
45 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
46 #if $celloptions.expect_cells != "0": |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
47 --expect-cells=$celloptions.expect_cells |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
48 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
49 --error-correct-threshold=$celloptions.error_correct_thresh |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
50 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
51 --method=$method |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
52 --plot-prefix=OUT |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
53 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
54 $prime3 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
55 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
56 #if $log: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
57 --log='$out_log' |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
58 #end if |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
59 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
60 > '$out_whitelist' && |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
61 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
62 mkdir '${ out_html_report.files_path }' && |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
63 cp OUT_*.png '${ out_html_report.files_path }' && |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
64 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
65 echo "<html> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
66 <head></head><body> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
67 <h1>Cell and Count Metrics</h1> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
68 <img src=\"OUT_cell_barcode_count_density.png\" ><br /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
69 <img src=\"OUT_cell_barcode_knee.png\" ><br /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
70 <img src=\"OUT_cell_barcode_counts.png\" ><br /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
71 </body></html>" > '$out_html_report' |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
72 && |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
73 mv OUT_cell_thresholds.tsv '$out_thresh' |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
74 ]]></command> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
75 <inputs> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
76 <conditional name="input_type"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
77 <param name="type" type="select" label="Library type"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
78 <option value="single">Single-end</option> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
79 <option value="paired">Paired-end</option> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
80 </param> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
81 <when value="single"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
82 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
83 </when> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
84 <when value="paired"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
85 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
86 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
87 <conditional name="barcode"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
88 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
89 <option value="first_read_only">Barcode on first read only</option> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
90 <option value="both_reads">Barcode on both reads</option> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
91 </param> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
92 <when value="first_read_only"/> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
93 <when value="both_reads"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
94 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read" |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
95 help="Use this option to specify the format of the UMI/barcode for |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
96 the second read pair if required."> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
97 </param> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
98 </when> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
99 </conditional> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
100 </when> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
101 </conditional> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
102 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read" |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
103 help="Use this option to specify the format of the UMI/barcode. Use Ns to |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
104 represent the random positions and Xs to indicate the bc positions. |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
105 Bases with Ns will be extracted and added to the read name. Remaining |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
106 bases, marked with an X will be reattached to the read."> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
107 </param> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
108 <param name="method" argument="--method" type="select" label="Count reads or UMIs" |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
109 help="Many published protocols rank CBs by the number of reads the CBs appear in. However you could also use the number of unique UMIs a CB is associated with. Note that this is still and approximation to the number of transcripts captured because the same UMI could be associated with two different transcripts and be counted as independent." > |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
110 <option value="reads" selected="true" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
111 <option value="umis" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
112 </param> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
113 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
114 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?" |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
115 truevalue="--3prime" falsevalue="" |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
116 help="By default the barcode is assumed to be on the 5' end of the read, but |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
117 use this option to specify that it is on the 3' end instead." /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
118 <param name="subset_reads" argument="--subset-reads" type="integer" min="0" value="0" label="Use the first N reads to automatically identify the true cell barcodes." /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
119 <conditional name="celloptions" > |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
120 <param name="use_cell_opts" type="select" label="Cell parameters" > |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
121 <option value="defaults" selected="True">Use Defaults</option> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
122 <option value="advanced">Advanced Options</option> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
123 </param> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
124 <when value="defaults"/> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
125 <when value="advanced"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
126 <param name="set_cell_number" type="integer" min="0" value="0" label="Specify the number of cell barcodes to accept" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
127 <param name="expect_cells" type="integer" min="0" value="0" label="Prior expectation on the upper limit on the number of cells sequenced" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
128 <param name="error_correct_thresh" type="integer" min="0" value="0" label="Hamming distance for correction of barcodes to whilelist barcodes. Set to zero to generate no error correcting metrics." /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
129 </when> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
130 </conditional> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
131 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue="" |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
132 help="Choose if you want to generate a text file containing logging information." /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
133 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
134 </inputs> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
135 <outputs> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
136 <data name="out_whitelist" format="tabular" label="${tool.name} on ${on_string}: Whitelist"/> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
137 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" > |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
138 <filter>log</filter> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
139 </data> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
140 <data name="out_html_report" format="html" label="${tool.name} on ${on_string}: Webpage" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
141 <data name="out_thresh" format="tabular" label="${tool.name} on ${on_string}: TSV Cell Thresholds" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
142 </outputs> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
143 <tests> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
144 <test expect_num_outputs="3"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
145 <param name="type" value="single" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
146 <param name="input_single" value="t_R2.fastq.gz" ftype="fastq" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
147 <param name="bc_pattern" value="CCCCCCCCNNNNNNNN" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
148 <param name="method" value="reads" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
149 <param name="prime3" value="true" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
150 <output name="out_whitelist" file="out_wl_single.txt" lines_diff="40" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
151 <output name="out_thresh" file="out_wl_single.tresh.tab" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
152 <output name="out_html_report" file="out_wl_single.html" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
153 </test> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
154 <test expect_num_outputs="4"> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
155 <param name="type" value="paired" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
156 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
157 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
158 <param name="barcode_select" value="both_reads" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
159 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
160 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
161 <param name="method" value="reads" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
162 <param name="prime3" value="false" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
163 <param name="use_cell_opts" value="advanced" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
164 <param name="expect_cells" value="5" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
165 <param name="error_correct_thresh" value="3" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
166 <param name="log" value="true" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
167 <output name="out_whitelist" file="out_wl_paired.txt" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
168 <output name="out_log" file="out_wl_paired.log" lines_diff="40" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
169 <output name="out_html_report" file="out_wl_paired.html" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
170 <output name="out_thresh" file="out_wl_paired.tresh.tab" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
171 </test> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
172 </tests> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
173 <help><![CDATA[ |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
174 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
175 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
176 UMI-tools whitelist - Extract barcodes from fastq |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
177 ================================================== |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
178 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
179 Purpose |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
180 ------- |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
181 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
182 Extract cell barcodes and identify the most likely true barcodes using |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
183 the 'knee' method. |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
184 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
185 Options |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
186 ------- |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
187 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
188 --bc-pattern |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
189 This should be used where the barcodes are always in the same |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
190 place in the read. |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
191 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
192 - N = UMI position (required) |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
193 - C = cell barcode position (optional) |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
194 - X = sample position (optional) |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
195 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
196 Bases with Ns and Cs will be extracted and added to the read |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
197 name. The corresponding sequence qualities will be removed from |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
198 the read. Bases with an X will be reattached to the read. |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
199 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
200 E.g. If the pattern is NNNNCC, |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
201 Then the read: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
202 @HISEQ:87:00000000 read1 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
203 AAGGTTGCTGATTGGATGGGCTAG |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
204 DA1AEBFGGCG01DFH00B1FF0B |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
205 + |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
206 will become: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
207 @HISEQ:87:00000000_TT_AAGG read1 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
208 GCTGATTGGATGGGCTAG |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
209 1AFGGCG01DFH00B1FF0B |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
210 + |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
211 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
212 where 'TT' is the cell barcode and 'AAGG' is the UMI. |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
213 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
214 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
215 --set-cell-number |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
216 Use this option to explicity set the number of cell barcodes |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
217 which should be accepted. Note that the exact number of cell |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
218 barcodes in the outputted whitelist may be slightly less than |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
219 this if there are multiple cells observed with the same |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
220 frequency at the threshold between accepted and rejected cell |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
221 barcodes. |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
222 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
223 --expect-cells=[EXPECTED_CELLS] |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
224 An upper limit estimate for the number of inputted cells. The knee |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
225 method will now select the first threshold (order ascendingly) |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
226 which results in the number of cell barcodes accepted being <= |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
227 EXPECTED_CELLS and > EXPECTED_CELLS * 0.1. |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
228 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
229 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
230 --bc-pattern2 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
231 Use this option to specify the format of the UMI/barcode for |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
232 the second read pair if required. If --bc-pattern2 is not |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
233 supplied, this defaults to the same pattern as --bc-pattern |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
234 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
235 --3prime |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
236 By default the barcode is assumed to be on the 5' end of the read, but |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
237 use this option to sepecify that it is on the 3' end instead |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
238 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
239 Usage: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
240 ------ |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
241 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
242 For single ended reads: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
243 umi_tools whitelist --bc-pattern=[PATTERN] -L extract.log |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
244 [OPTIONS] |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
245 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
246 reads from stdin and outputs to stdout. |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
247 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
248 For paired end reads where the cell barcodes is split across the read pairs: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
249 umi_tools whitelist --bc-pattern=[PATTERN] |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
250 --bc-pattern2=[PATTERN] --read2-in=[FASTQIN] -L extract.log |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
251 [OPTIONS] |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
252 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
253 reads end one from stdin and end two from FASTQIN and outputs to stdin |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
254 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
255 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
256 Output: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
257 ------- |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
258 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
259 The whitelist is outputted as 4 tab-separated columns: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
260 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
261 1. whitelisted cell barcode |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
262 2. Other cell barcode(s) (comma-separated) to correct to the |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
263 whitelisted barcode |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
264 3. Count for whitelisted cell barcodes |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
265 4. Count(s) for the other cell barcode(s) (comma-separated) |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
266 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
267 example output: |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
268 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
269 AAAAAA AGAAAA 146 1 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
270 AAAATC 22 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
271 AAACAT 21 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
272 AAACTA AAACTN,GAACTA 27 1,1 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
273 AAATAC 72 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
274 AAATCA GAATCA 37 3 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
275 AAATGT AAAGGT,CAATGT 41 1,1 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
276 AAATTG CAATTG 36 1 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
277 AACAAT 18 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
278 AACATA 24 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
279 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
280 If --error-correct-threshold is set to 0, columns 2 and 4 will be empty. |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
281 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
282 |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
283 ]]></help> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
284 <expand macro="citations" /> |
b911124762a8
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
|
285 </tool> |