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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
author jjohnson
date Tue, 18 Feb 2020 14:48:51 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
1 <tool id="netmhc" name="netMHC" version="4.0.0">
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
2 <description>MHC Binding prediction</description>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
3 <requirements>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
4 <requirement type="package" version="4.0">netMHC</requirement>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
5 </requirements>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
6 <stdio>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
7 <exit_code range="1:" />
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
8 </stdio>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
9 <configfiles>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
10 <configfile name="format_out"><![CDATA[
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
11 import sys
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
12 import re
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
13 if len(sys.argv) != 3:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
14 print >> sys.stderr, "python script.py netMHC_output_tsv output_file"
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
15 exit(4);
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
16 hpat = '^\s*(pos)\s+(HLA)\s+(peptide)\s+(Core)\s+(Offset)\s+(I_pos)\s+(I_len)\s+(D_pos)\s+(D_len)\s+(iCore)\s+(Identity)\s+(1-log50k.aff.)\s+(Affinity.nM.)\s+(%Rank)\s+(BindLevel)\s*$'
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
17 epat = '^\s*(\d+)\s+(\S+)\s+([A-Z]+)\s+([-_A-Z]*)\s+([0-9]+)\s+([0-9]+)\s+([0-9]+)\s+([0-9]+)\s+([0-9]+)\s+([A-Z]+)\s+(\S+)\s+([0-9.]+)\s+([0-9.]+)\s+([0-9.]+).*?([SWB]*)$'
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
18 cnt = 0
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
19 try:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
20 wh = open(sys.argv[2],'w')
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
21 fh = open(sys.argv[1],'r')
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
22 for i,line in enumerate(fh):
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
23 line = line.rstrip()
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
24 if not line:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
25 continue
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
26 ## print >> sys.stderr, line
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
27 m = re.match(epat,line)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
28 if m:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
29 ## print >> sys.stderr, str(m.groups())
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
30 wh.write("%s\n" % '\t'.join([x if x else '' for x in m.groups()]))
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
31 cnt += 1
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
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diff changeset
32 elif cnt == 0:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
33 m = re.match(hpat,line)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
34 if m:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
35 ## print >> sys.stderr, str(m.groups())
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
36 wh.write("#%s\n" % '\t'.join(m.groups()))
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
37 cnt += 1
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
38 wh.close()
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
39 fh.close()
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
40 except Exception, e:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
41 print sys.stderr, "error: %s" % e
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
42 exit(3)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
43 ]]>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
44 </configfile>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
45 <configfile name="format_tsv"><![CDATA[
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
46 #!/usr/bin/env python
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
47 import sys
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
48 if len(sys.argv) != 3:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
49 print >> sys.stderr, "python script.py netMHC_xls output_file"
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
50 exit(4);
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
51 try:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
52 wh = open(sys.argv[2],'w')
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
53 fh = open(sys.argv[1],'r')
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
54 for n,line in enumerate(fh):
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
55 if n > 1:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
56 wh.write(line)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
57 if n == 0:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
58 alleles = line.rstrip('\n').split('\t')
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
59 if n == 1:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
60 hdr = line.rstrip('\n').split('\t')
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
61 wh.write('#%s\n' % '\t'.join([' '.join([alleles[i - i%3],hdr[i]]).strip() for i in range(len(hdr))]))
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
62 wh.close()
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
63 fh.close()
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
64 except Exception, e:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
65 print sys.stderr, "error: %s" % e
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
66 exit(3)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
67 ]]>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
68 </configfile>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
69 </configfiles>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
70 <command><![CDATA[
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
71 ### netMHC -tdir tmp -f OS11Fusion.fa -a 'HLA-A3001,HLA-A0301,HLA-B4201,HLA-B5802,HLA-C0602' -l '8,9,10' -xls -xlsfile OS11Fusion.xls > OS11_netMHC.out
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
72 #set $valid_alleles = [
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
73 'BoLA-AW10',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
74 'BoLA-D18.4',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
75 'BoLA-HD6',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
76 'BoLA-JSP.1',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
77 'BoLA-T2C',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
78 'BoLA-T2a',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
79 'BoLA-T2b',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
80 'H-2-Db',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
81 'H-2-Dd',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
82 'H-2-Kb',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
83 'H-2-Kd',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
84 'H-2-Kk',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
85 'H-2-Ld',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
86 'HLA-A0101',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
87 'HLA-A0201',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
88 'HLA-A0202',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
89 'HLA-A0203',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
90 'HLA-A0205',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
91 'HLA-A0206',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
92 'HLA-A0207',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
93 'HLA-A0211',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
94 'HLA-A0212',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
95 'HLA-A0216',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
96 'HLA-A0217',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
97 'HLA-A0219',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
98 'HLA-A0250',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
99 'HLA-A0301',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
100 'HLA-A0302',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
101 'HLA-A0319',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
102 'HLA-A1101',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
103 'HLA-A2301',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
104 'HLA-A2402',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
105 'HLA-A2403',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
106 'HLA-A2501',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
107 'HLA-A2601',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
108 'HLA-A2602',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
109 'HLA-A2603',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
110 'HLA-A2902',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
111 'HLA-A3001',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
112 'HLA-A3002',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
113 'HLA-A3101',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
114 'HLA-A3201',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
115 'HLA-A3207',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
116 'HLA-A3215',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
117 'HLA-A3301',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
118 'HLA-A6601',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
119 'HLA-A6801',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
120 'HLA-A6802',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
121 'HLA-A6823',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
122 'HLA-A6901',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
123 'HLA-A8001',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
124 'HLA-B0702',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
125 'HLA-B0801',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
126 'HLA-B0802',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
127 'HLA-B0803',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
128 'HLA-B1401',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
129 'HLA-B1402',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
130 'HLA-B1501',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
131 'HLA-B1502',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
132 'HLA-B1503',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
133 'HLA-B1509',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
134 'HLA-B1517',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
135 'HLA-B1801',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
136 'HLA-B2705',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
137 'HLA-B2720',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
138 'HLA-B3501',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
139 'HLA-B3503',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
140 'HLA-B3701',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
141 'HLA-B3801',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
142 'HLA-B3901',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
143 'HLA-B4001',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
144 'HLA-B4002',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
145 'HLA-B4013',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
146 'HLA-B4201',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
147 'HLA-B4402',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
148 'HLA-B4403',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
149 'HLA-B4501',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
150 'HLA-B4506',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
151 'HLA-B4601',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
152 'HLA-B4801',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
153 'HLA-B5101',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
154 'HLA-B5301',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
155 'HLA-B5401',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
156 'HLA-B5701',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
157 'HLA-B5703',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
158 'HLA-B5801',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
159 'HLA-B5802',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
160 'HLA-B7301',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
161 'HLA-B8101',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
162 'HLA-B8301',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
163 'HLA-C0303',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
164 'HLA-C0401',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
165 'HLA-C0501',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
166 'HLA-C0602',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
167 'HLA-C0701',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
168 'HLA-C0702',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
169 'HLA-C0802',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
170 'HLA-C1203',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
171 'HLA-C1402',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
172 'HLA-C1502',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
173 'HLA-E0101',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
174 'HLA-E0103',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
175 'Mamu-A01',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
176 'Mamu-A02',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
177 'Mamu-A07',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
178 'Mamu-A11',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
179 'Mamu-A20102',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
180 'Mamu-A2201',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
181 'Mamu-A2601',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
182 'Mamu-A70103',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
183 'Mamu-B01',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
184 'Mamu-B03',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
185 'Mamu-B08',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
186 'Mamu-B1001',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
187 'Mamu-B17',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
188 'Mamu-B3901',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
189 'Mamu-B52',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
190 'Mamu-B6601',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
191 'Mamu-B8301',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
192 'Mamu-B8701',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
193 'Patr-A0101',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
194 'Patr-A0301',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
195 'Patr-A0401',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
196 'Patr-A0701',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
197 'Patr-A0901',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
198 'Patr-B0101',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
199 'Patr-B1301',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
200 'Patr-B2401',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
201 'SLA-10401',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
202 'SLA-10701',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
203 'SLA-20401',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
204 'SLA-30401',
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
205 ]
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
206 #set $allelelist = []
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
207 #set $unknown_alleles = []
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
208 #if $alleles.allelesrc == 'history':
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
209 #for $line in open(str($alleles.allele_file)):
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
210 #set $fields = $line.strip().split(',')
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
211 #set $allele = $fields[0].strip()
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
212 #if $allele in $valid_alleles:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
213 $allelelist.append($allele)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
214 #else
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
215 $unknown_alleles.append($allele)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
216 #end if
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
217 #end for
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
218 #else:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
219 #for $word in str($alleles.allele_text).strip().split():
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
220 #set $fields = $word.strip().split(',')
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
221 #set $allele = $fields[0].strip()
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
222 #if $allele in $valid_alleles:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
223 $allelelist.append($allele)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
224 #else
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
225 $unknown_alleles.append($allele)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
226 #end if
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
227 #end for
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
228 #end if
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
229 #if len($allelelist) < 1
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
230 echo 'No netMHC alleles';
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
231 echo "unknown: $unknown_alleles";
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
232 exit 1;
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
233 #else
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
234 echo "netMHC alleles: $allelelist"
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
235 && echo "unknown alleles: $unknown_alleles"
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
236 && echo "peptide lengths: $lengths"
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
237 #set $alist = ','.join($allelelist)
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
238 && netMHC -tdir tmp -f "$seq_fasta" -a '$alist' -l '$lengths' $sort
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
239 #if $threshold_sec.rth:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
240 -rth $threshold_sec.rth
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
241 #end if
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
242 #if $threshold_sec.rlt:
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
243 -rlt $threshold_sec.rlt
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
244 #end if
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
245 -xls -xlsfile results.tsv > results.out
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
246 && python $format_out results.out $output
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
247 && python $format_tsv results.tsv $results_tsv
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
248 #end if
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
249 ]]></command>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
250 <inputs>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
251 <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
252 <conditional name="alleles">
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
253 <param name="allelesrc" type="select" label="Alleles">
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
254 <option value="history">From history</option>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
255 <option value="entry">Entered</option>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
256 </param>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
257 <when value="history">
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
258 <param name="allele_file" type="data" format="txt" label="Alleles file"/>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
259 <help>The dataset should have on allele per line: HLA-A0201</help>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
260 </when>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
261 <when value="entry">
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
262 <param name="allele_text" type="text" label="Alleles">
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
263 <help>Enter alleles separated by commas: HLA-A0201,HLA-B0702</help>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
264 <validator type="regex" message="IDs separted by commas">^(\S+)(,\S+)*$</validator>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
265 </param>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
266 </when>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
267 </conditional>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
268 <param name="lengths" type="select" multiple="true" label="peptide lengths for prediction">
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
269 <help>Used for any alleles which don't include specified lengths</help>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
270 <option value="8">8</option>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
271 <option value="9">9</option>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
272 <option value="10">10</option>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
273 <option value="11">11</option>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
274 <option value="12">12 (unvalidated)</option>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
275 <option value="13">13 (unvalidated)</option>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
276 <option value="14">14 (unvalidated)</option>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
277 </param>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
278 <param name="sort" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Sort output on descending affinity"/>
bb25a4e5f211 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/netmhc commit 3bf9a39fe11622806ac6b032ba4fc6139a003580"
jjohnson
parents:
diff changeset
279 <section name="threshold_sec" expanded="false" title="Adjust Thresholds">
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280 <param name="rth" type="float" value="0.500000" optional="true" label="Threshold for high binding peptides (%Rank)"/>
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281 <param name="rlt" type="float" value="2.000000" optional="true" label="Threshold for low binding peptides (%Rank)"/>
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282 </section>
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283 </inputs>
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284 <outputs>
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285 <data name="output" format="tabular" label="${tool.name} on ${on_string} Binding Scores"/>
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286 <data name="results_tsv" format="tabular" label="${tool.name} on ${on_string} Peptide Summary"/>
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287 </outputs>
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288 <help><![CDATA[
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289 **NetMHC**
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290
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291 http://www.cbs.dtu.dk/services/NetMHC/
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292
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293 NetMHC 4.0 predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANNs).
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294
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295 ANNs have been trained for 78 different Human MHC (HLA) alleles representing all 12 HLA A and B Supertypes as defined by Lund et al. (2004). Furthermore 41 animal (Monkey, Cattle, Pig, and Mouse) allele predictions are available.
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296
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297 Prediction values are given in nM IC50 values.
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298
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299 Predictions of lengths 8-14: Predictions can be made for lengths between 8 and 14 for all alleles using an novel approximation algorithm using ANNs trained on 9mer peptides. Probably because of the limited amount of available 10mer data this method has a better predictive value than ANNs trained on 10mer data.
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300 Predictions of peptides longer than 11 have not been extensively validated!
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301 Caution should be taken for 8mer predictions as some alleles might not bind 8mers to any significant extend.
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302
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303 Strong and weak binding peptides are indicated in the output. In the selection window for HLA alleles, the recommended allele for each HLA supertype is indicated.
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304
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305 **Inputs**
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306
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307 A fasta file of peptide sequences in your history
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308
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309 A list Alleles entered as text or from a history dataset, one allele per line
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310
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311 **Outputs**
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312
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313 **Binding Scores**
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314
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315 ==== ========= ========== ========= ====== ===== ===== ===== ===== ========== ============= ============= ============ ===== =========
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316 #pos HLA peptide Core Offset I_pos I_len D_pos D_len iCore Identity 1-log50k(aff) Affinity(nM) %Rank BindLevel
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317 ==== ========= ========== ========= ====== ===== ===== ===== ===== ========== ============= ============= ============ ===== =========
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318 16 HLA-A3001 HGRWDTNCA HGRWDTNCA 0 0 0 0 0 HGRWDTNCA SOGA2_CREB3L1 0.487 257.58 0.90 WB
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319 1 HLA-A3001 LQNELERLK LQNELERLK 0 0 0 0 0 LQNELERLK SOGA2_CREB3L1 0.242 3647.96 6.00
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320 16 HLA-A3001 HGRWDTNCAP HGRWTNCAP 0 0 0 4 1 HGRWDTNCAP SOGA2_CREB3L1 0.185 6739.05 9.50
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321 6 HLA-C0602 ERLKEMQSM ERLKEMQSM 0 0 0 0 0 ERLKEMQSM SOGA2_CREB3L1 0.382 798.43 0.40 SB
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322 12 HLA-C0602 QSMEHGRWD QSMEHGRWD 0 0 0 0 0 QSMEHGRWD SOGA2_CREB3L1 0.229 4177.34 1.50 WB
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323 3 HLA-C0602 NELERLKEM NELERLKEM 0 0 0 0 0 NELERLKEM SOGA2_CREB3L1 0.209 5224.29 1.80 WB
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324 20 HLA-A3001 DTNCAPSW DTNCA-PSW 0 5 1 0 0 DTNCAPSW SOGA2_CREB3L1 0.050 29125.62 60.00
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325 20 HLA-C0602 DTNCAPSW DT-NCAPSW 0 2 1 0 0 DTNCAPSW SOGA2_CREB3L1 0.005 47120.04 90.00
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326 ==== ========= ========== ========= ====== ===== ===== ===== ===== ========== ============= ============= ============ ===== =========
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327
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328
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329
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330 **Peptide Summary**
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331
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332 ==== ========= ============= ============ ============== ============== ============ ============== ============== =========== =========
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333 #Pos Peptide ID HLA-A3001 nM HLA-A3001 Rank HLA-A3001 Core HLA-C0602 nM HLA-C0602 Rank HLA-C0602 Core H_Avg_Ranks N_binders
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334 ==== ========= ============= ============ ============== ============== ============ ============== ============== =========== =========
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335 16 HGRWDTNCA SOGA2_CREB3L1 257.6 0.900 HGRWDTNCA 35765.3 25.000 HGRWDTNCA 4.124 1
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336 20 DTNCAPSW SOGA2_CREB3L1 29125.6 60.000 DTNCA_PSW 47120.0 90.000 DT_NCAPSW 6.909 0
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337 ==== ========= ============= ============ ============== ============== ============ ============== ============== =========== =========
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338
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339
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340 ]]></help>
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341 <citations>
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342 <citation type="doi">10.1093/nar/gkn202</citation>
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343 <citation type="doi">10.1093/bioinformatics/btn128</citation>
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344 <citation type="doi">10.1093/bioinformatics/btn100</citation>
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345 <citation type="doi">10.1110/ps.0239403</citation>
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346 </citations>
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347 </tool>