Mercurial > repos > iuc > crosscontamination_barcode_filter
annotate crosscontamination_barcode_filter.xml @ 0:582b7bd4ae4c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
author | iuc |
---|---|
date | Thu, 24 Jan 2019 09:52:58 -0500 |
parents | |
children | 253c9448f524 |
rev | line source |
---|---|
0
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
1 <tool id="crosscontamination_barcode_filter" name="Cross-contamination Barcode Filter" version="@VERSION@"> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
2 <description>for use in plate-based barcoded analyses</description> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
3 <macros> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
4 <token name="@VERSION@">0.1</token> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
5 <macro name="assert_conts" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
6 <assert_contents> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
7 <has_text text="/CreationDate" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
8 <has_text text="/Producer" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
9 <has_line line="startxref" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
10 <has_line line="%%EOF" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
11 </assert_contents> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
12 </macro> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
13 <macro name="sanitize_batch"> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
14 <sanitizer invalid_char=""> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
15 <valid initial="string.digits"> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
16 <add value=","/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
17 </valid> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
18 </sanitizer> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
19 </macro> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
20 <macro name="sanitize_regex"> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
21 <sanitizer invalid_char=""> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
22 <valid initial="string.letters,string.digits"> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
23 <add value="!"/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
24 <add value="="/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
25 <add value="-"/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
26 <add value="."/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
27 <add value="*"/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
28 <add value="?"/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
29 <add value="+"/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
30 <add value="\\"/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
31 <add value="_"/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
32 <add value="["/> <!-- left square bracket, e.g subselecting from vec[1] --> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
33 <add value="]"/> <!-- right square bracket --> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
34 <add value="("/> <!-- left parenthesis --> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
35 <add value=")"/> <!-- right parenthesis --> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
36 </valid> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
37 </sanitizer> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
38 </macro> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
39 </macros> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
40 <requirements> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
41 <requirement type="package" version="2.2.1" >r-ggplot2</requirement> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
42 </requirements> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
43 <version_command><![CDATA[ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
44 Rscript '$__tool_directory__/scripts/crosscontamination_filter.R' | head -1 | cut -d' ' -f 2 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
45 ]]></version_command> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
46 <command detect_errors="exit_code"><![CDATA[ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
47 Rscript '$__tool_directory__/scripts/crosscontamination_filter.R' '$crossconf' |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
48 ]]></command> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
49 <configfiles> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
50 <configfile name="crossconf"><![CDATA[ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
51 script.dir = '$__tool_directory__/scripts' |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
52 input_matrix <- read.table( |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
53 '$input_table', |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
54 stringsAsFactors = F, |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
55 na.strings=c("NA", "-", "?", "."), |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
56 header=TRUE, |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
57 row.names=1 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
58 ) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
59 input_matrix[is.na(input_matrix)] <- 0 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
60 #if str($inbuilt_spec.select_use) == "mpi_sagar": |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
61 spec = list( |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
62 barcodes = '$input_barcodes', |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
63 format = list( |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
64 "1-96" = c(1,3,5,7), |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
65 "97-192" = c(2,4,6,8) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
66 ), |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
67 plates = list( |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
68 "1" = c(1,2,3,4), |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
69 "2" = c(5,6,7,8) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
70 ) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
71 ) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
72 #elif str($inbuilt_spec.select_use) == "custom": |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
73 spec = list( |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
74 barcodes = '$input_barcodes', |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
75 format = list( |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
76 #for $i, $s in enumerate($inbuilt_spec.barcode_format) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
77 "${s.range_start}-${s.range_end}" = c( ${s.batches} ) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
78 #if $i < len(list($inbuilt_spec.barcode_format)) - 1 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
79 , |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
80 #end if |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
81 #end for |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
82 ), |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
83 plates = list( |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
84 #for $i, $s in enumerate($inbuilt_spec.plate_format) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
85 "${s.plate}" = c( ${s.batches} ) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
86 #if $i < len(list($inbuilt_spec.plate_format)) - 1 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
87 , |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
88 #end if |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
89 #end for |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
90 ) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
91 ) |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
92 #end if |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
93 regex.extract = '$advanced.regex_extract' |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
94 regex.display = '$advanced.regex_display' |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
95 out.pdf = '$out_plots' |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
96 out.table = '$out_table' |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
97 ]]> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
98 </configfile> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
99 </configfiles> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
100 <inputs> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
101 <param name="input_table" type="data" format="tsv,tabular" label="Input Matrix" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
102 <param name="input_barcodes" type="data" format="tsv,tabular,txt" label="Complete Barcodes" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
103 <conditional name="inbuilt_spec" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
104 <param name="select_use" type="select" label="Plate Protocol" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
105 <option value="mpi_sagar">CelSeq2 Plate Protocol (Sagar)</option> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
106 <option value="custom">Custom</option> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
107 </param> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
108 <when value="mpi_sagar" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
109 <when value="custom"> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
110 <repeat name="barcode_format" title="Barcode Format" help="e.g. Batches 1 and 4 use barcodes 1-100 in the Barcodes file, and Batches 2 and 3 use barcodes 101-200 in the Barcodes file; specify '1' and '100' as Range values, and '1,4' as Batch values, and in the next format specify '101' and '200' as Range values and '2,3' as Batch values" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
111 <param name="range_start" type="integer" min="1" value="1" label="Barcode Range: Start" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
112 <param name="range_end" type="integer" min="2" value="100" label="Barcode Range: End" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
113 <param name="batches" type="text" value="1,4" label="Batches utilizing this Range" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
114 <expand macro="sanitize_batch" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
115 </param> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
116 </repeat> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
117 <repeat name="plate_format" title="Plate Format" help="e.g. Plate 1 encompasses Batches 1-4, and Plate 2 encompasses Batches 5-8; specify '1' as a Plate value, and '1,2,3,4' as Batch values, and in the next format specify '2' as a Plate value and '5,6,7,8' as Batch values"> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
118 <param name="plate" type="integer" min="1" value="1" label="Plate Number" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
119 <param name="batches" type="text" value="1,2,3,4" label="Batches within this Plate Number" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
120 <expand macro="sanitize_batch" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
121 </param> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
122 </repeat> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
123 </when> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
124 </conditional> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
125 <section name="advanced" expanded="false" title="RegEx Parameters" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
126 <param name="regex_extract" type="text" value=".*P(\\d)_(\\d)_([ACTG]+)" label="RegEx to extract Plate, Batch, and Barcodes from headers" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
127 <expand macro="sanitize_regex" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
128 </param> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
129 <param name="regex_display" type="text" value="P\\1_B\\2_\\3" label="RegEx to replace Plate, Batch, and Barcodes from headers" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
130 <expand macro="sanitize_regex" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
131 </param> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
132 </section> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
133 </inputs> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
134 <outputs> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
135 <data name="out_plots" format="pdf" label="${tool.name} on ${on_string}: Plots" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
136 <data name="out_table" format="tabular" label="${tool.name} on ${on_string}: Filtered Table" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
137 </outputs> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
138 <tests> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
139 <test><!-- Inbuilt MPI --> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
140 <param name="input_table" value="out3.subtable" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
141 <param name="input_barcodes" value="celseq_barcodes.192.raw" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
142 <conditional name="inbuilt_spec" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
143 <param name="select_use" value="mpi_sagar" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
144 </conditional> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
145 <output name="out_plots" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
146 <expand macro="assert_conts" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
147 </output> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
148 <output name="out_table" value="test.table" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
149 </test> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
150 <test><!-- Plate and Lane test --> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
151 <param name="input_table" value="out3.subtable" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
152 <param name="input_barcodes" value="celseq_barcodes.192.raw" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
153 <conditional name="inbuilt_spec" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
154 <param name="select_use" value="custom" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
155 <repeat name="barcode_format" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
156 <param name="range_start" value="1"/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
157 <param name="range_end" value="96" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
158 <param name="batches" value="1,3,5,7" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
159 </repeat> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
160 <repeat name="barcode_format" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
161 <param name="range_start" value="97"/> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
162 <param name="range_end" value="192" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
163 <param name="batches" value="2,4,6,8" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
164 </repeat> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
165 <repeat name="plate_format" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
166 <param name="plate" value="1" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
167 <param name="batches" value="1,2,3,4" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
168 </repeat> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
169 <repeat name="plate_format" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
170 <param name="plate" value="2" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
171 <param name="batches" value="5,6,7,8" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
172 </repeat> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
173 </conditional> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
174 <output name="out_plots" > |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
175 <expand macro="assert_conts" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
176 </output> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
177 <output name="out_table" value="test.table" /> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
178 </test> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
179 </tests> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
180 <help><![CDATA[ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
181 Cross-contamination Filter Plot |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
182 ################################### |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
183 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
184 For a set of barcodes and an experimental setup that uses a subset of these barcodes for each batch, this tool compares each batch against the full range of barcodes in order to determine whether any cross-contamination between batches has occured. |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
185 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
186 If a significant number of transcripts are shown in a batch for cell barcodes that were not designed for that batch, then this tool will show that. In the below plot, we can see that there is no significant cross-contamination taking place (pre-filter), and so we can filter out the false barcodes (post-filter). |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
187 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
188 .. image:: $PATH_TO_IMAGES/crosscontam_pretopost.png |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
189 :scale: 50 % |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
190 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
191 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
192 Example |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
193 ~~~~~~~~ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
194 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
195 Consider the following experimental setup, with a list of 100 possible barcodes, used over 3 sequencing plates, with each plate containing 4 unique batches, and each plate using a specific subset of the 100 barcodes. |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
196 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
197 :: |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
198 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
199 Barcodes |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
200 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
201 1 - 10 | AAA AAC AAT AAG ACA AGA ATA CAC GAG TAT |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
202 11 - 20 | CCC CCA CCT CCG CTC CGC TCT GCG TCT CGT |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
203 . |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
204 . |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
205 91 -100 | TTT TAT TCT TGT TTA TTC TTG TCC TGG TAA |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
206 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
207 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
208 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
209 Plate 1 +-------+-------+-------+-------+ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
210 | B1 | B2 | B3 | B4 | |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
211 +-------+-------+-------+-------+ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
212 1-50 51-100 51-100 1-50 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
213 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
214 Plate 2 +-------+-------+-------+-------+ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
215 | B5 | B6 | B7 | B8 | |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
216 +-------+-------+-------+-------+ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
217 1-40 41-80 1-40 41-80 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
218 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
219 Plate 3 +-------+-------+-------+-------+ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
220 | B9 | B10 | B11 | B12 | |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
221 +-------+-------+-------+-------+ |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
222 1-40 41-80 1-40 41-80 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
223 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
224 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
225 **** |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
226 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
227 The above plate and barcoding setup can be more textually represented by specifying barcode ranges and plate numbers, with each denoting which batch numbers they describe as outlined below: |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
228 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
229 :: |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
230 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
231 *Barcodes → Batches* |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
232 1- 50: B1, B4 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
233 51-100: B2, B3 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
234 1- 40: B5, B7, B9 , B11 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
235 41- 80: B6, B8, B10, B12 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
236 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
237 *Plates → Batches* |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
238 1: B1, B2 , B3 , B4 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
239 2: B5, B6 , B7 , B8 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
240 3: B9, B10, B11, B12 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
241 |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
242 ]]></help> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
243 <citations> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
244 <citation type="doi">10.1007/978-1-4939-7768-0_15</citation> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
245 </citations> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
246 </tool> |
582b7bd4ae4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter commit 6f73edc667e61fabdab8b24a7ff40942588fee5b
iuc
parents:
diff
changeset
|
247 |