Mercurial > repos > drosofff > msp_sr_bowtie

comparison sRbowtie.xml @ 22:764181d43c36 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 1793456e6d76453825d92c76ca1051f6eccde0ab
author drosofff
date Tue, 27 Jun 2017 04:33:53 -0400
parents f752a90d266f
children 411b6453b5d0
comparison
equal deleted inserted replaced
21:f752a90d266f 22:764181d43c36
16 #set format = "-q" 16 #set format = "-q"
17 #end if 17 #end if
18 18
19 ## set the method_prefix 19 ## set the method_prefix
20 #if $method == "RNA": 20 #if $method == "RNA":
21 #set method_prefix = "-v %s -M 1 --best --strata --norc" % (str($v_mismatches)) 21 #set method_prefix = "-v %s -M 1 --best --strata --norc" % str($v_mismatches)
22 #elif $method == "unique": 22 #elif $method == "unique":
23 #set method_prefix = "-v %s -m 1" % (str($v_mismatches)) 23 #set method_prefix = "-v %s -m 1" % str($v_mismatches)
24 #elif $method == "multiple": 24 #elif $method == "multiple":
25 #set method_prefix = "-v %s -M 1 --best --strata" % (str($v_mismatches)) 25 #set method_prefix = "-v %s -M 1 --best --strata" % str($v_mismatches)
26 #elif $method == "k_option": 26 #elif $method == "k_option":
27 #set method_prefix = "-v %s -k 1 --best" % (str($v_mismatches)) 27 #set method_prefix = "-v %s -k 1 --best" % str($v_mismatches)
28 #elif $method == "n_option": 28 #elif $method == "n_option":
29 #set method_prefix = "-n %s -M 1 --best" % (str($v_mismatches)) 29 #set method_prefix = "-n %s -M 1 --best" % str($v_mismatches)
30 #elif $method == "a_option": 30 #elif $method == "a_option":
31 #set method_prefix = "-v %s -a --best" % (str($v_mismatches)) 31 #set method_prefix = "-v %s -a --best" % str($v_mismatches)
32 #end if 32 #end if
33 33
34 ## set the extra_output 34 ## set the extra_output
35 #if $additional_fasta == "No": 35 #if $additional_fasta == "No":
36 #set extra_output = "" 36 #set extra_output = ""