Mercurial > repos > lparsons > cutadapt

comparison cutadapt.xml @ 33:135b80fb1ac2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 7143af903be8405ca77d524b343e0973304be693
author iuc
date Fri, 14 Oct 2022 12:50:14 +0000
parents 5915ea1ec9b1
children 9845c649f41b
comparison
equal deleted inserted replaced
32:5915ea1ec9b1 33:135b80fb1ac2
16 #set read2 = "input_r" 16 #set read2 = "input_r"
17 #set paired = False 17 #set paired = False
18 #set library_type = str($library.type) 18 #set library_type = str($library.type)
19 #if $library_type == 'paired': 19 #if $library_type == 'paired':
20 #set paired = True 20 #set paired = True
21 #set input_1 = $library.input_1
22 #set input_2 = $library.input_2
23 ## Avoid the paired read input files sharing the same name, else the program still runs but
24 ## uses inaccurate results by using only 1 of 2 files.
21 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier)) 25 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.element_identifier))
22 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier)) 26 #set read2 = re.sub('[^\w\-\s]', '_', str($library.input_2.element_identifier))
23 #set input_1 = $library.input_1 27 #if read1 == read2:
24 #set input_2 = $library.input_2 28 #set read1 = read1 + "_1"
29 #set read2 = read2 + "_2"
30 #end if
25 #else if $library_type == 'paired_collection' 31 #else if $library_type == 'paired_collection'
26 #set paired = True 32 #set paired = True
27 #set input_1 = $library.input_1.forward 33 #set input_1 = $library.input_1.forward
28 #set input_2 = $library.input_1.reverse 34 #set input_2 = $library.input_1.reverse
29 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_1" 35 #set read1 = re.sub('[^\w\-\s]', '_', str($library.input_1.name)) + "_1"