Mercurial > repos > jjohnson > iedb_api

annotate iedb_api.xml @ 4:a14128950578 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
author jjohnson
date Fri, 28 Feb 2020 15:45:14 -0500
parents 153d5fa7af53
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
1 <tool id="iedb_api" name="IEDB" version="2.15.0">
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
2 <description>MHC Binding prediction</description>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
3 <macros>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
4 <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples="">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
5 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
6 <param name="allelesrc" type="select" label="Alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
7 <option value="history">From history</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
8 <option value="entry">Entered</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
9 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
10 <when value="history">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
11 <param name="allele_file" type="data" format="txt" label="Alleles file">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
12 <help>The dataset should have on allele per line. The allele may be followed by an optional comma-separated list of peptide lengths, e.g.: @HLALEN_EXAMPLES@</help>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
13 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
14 </when>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
15 <when value="entry">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
16 <param name="allele_text" type="text" size="80" label="Alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
17 <help>Enter alleles separated by white space: @HLA_EXAMPLES@ (The peptide lengths may follow each allele: @HLALEN_EXAMPLES@)</help>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
18 <validator type="regex" message="Doesn't appear to be a valid allele">^@HLA_REGEX@(\s+@HLA_REGEX@)*$</validator>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
19 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
20 </when>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
21 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
22 </xml>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
23 </macros>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
24 <requirements>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
25 <requirement type="package" version="3.7">python</requirement>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
26 </requirements>
4
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
27
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
28 <command detect_errors="exit_code"><![CDATA[
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
29 #import re
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
30 python '${__tool_directory__}/iedb_api.py'
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
31 --prediction=$prediction.tool
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
32 --method=$prediction.method
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
33 #if $prediction.tool == 'bcell':
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
34 #if $prediction.window_size:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
35 -w $prediction.window_size
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
36 #end if
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
37 #else
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
38 #if $prediction.tool == 'processing' and $prediction.proteasome:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
39 --proteasome $prediction.proteasome
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
40 #end if
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
41 #if $prediction.alleles.allelesrc == 'history':
4
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
42 -A '$prediction.alleles.allele_file'
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
43 #else:
4
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
44 -A '$entered_alleles'
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
45 #end if
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
46 #end if
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
47
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
48 #if $sequence.seqsrc == 'fasta':
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
49 -i '$sequence.seq_fasta'
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
50 #else if $sequence.seqsrc == 'tabular':
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
51 -i '$sequence.seq_tsv'
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
52 -c #echo int(str($sequence.pep_col)) - 1
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
53 #if $sequence.id_col:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
54 -C #echo int(str($sequence.id_col)) - 1
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
55 #end if
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
56 #else:
4
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
57 -i '$entered_seqs' -c 1 -C 0
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
58 #end if
3
153d5fa7af53 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
jjohnson
parents: 2
diff changeset
59 -o '$output'
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
60 ]]></command>
4
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
61 <configfiles>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
62 <configfile name="entered_alleles"><![CDATA[#slurp
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
63 #if $prediction.tool != 'bcell' and $prediction.alleles.allelesrc == 'entry'
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
64 #for $word in str($prediction.alleles.allele_text).strip().split():
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
65 #if $word.find(',') > 0
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
66 $word
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
67 #else
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
68 #set $allele = $word + ',' + str($prediction.lengths)
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
69 $allele
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
70 #end if
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
71 #end for
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
72 #end if
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
73 ]]></configfile>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
74 <configfile name="entered_seqs"><![CDATA[#slurp
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
75 #if $sequence.seqsrc == 'entry'
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
76 #for $i, $seq in enumerate(str($sequence.seq_text).strip().split())
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
77 #set $seqid = $i + 1
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
78 #set $seqtext = '\t'.join([str($seqid),$seq.strip()])
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
79 $seqtext
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
80 #end for
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
81 #end if
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
82 ]]></configfile>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
83 </configfiles>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
84 <inputs>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
85 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
86 <param name="tool" type="select" label="Prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
87 <option value="mhci">MHC-I Binding</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
88 <option value="mhcii">MHC-II Binding</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
89 <option value="processing">MHC-I Processing</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
90 <option value="mhcnp">MHC-NP T-Cell Epitope</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
91 <option value="bcell">Antibody Epitope Prediction</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
92 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
93 <when value="mhci">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
94 <param name="method" type="select" label="prediction method">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
95 <option value="recommended" selected="true">recommended</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
96 <option value="consensus">consensus</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
97 <option value="netmhcpan">netmhcpan</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
98 <option value="ann">ann</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
99 <option value="smmpmbec">smmpmbec</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
100 <option value="smm">smm</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
101 <option value="comblib_sidney2008">comblib_sidney2008</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
102 <option value="netmhccons">netmhccons</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
103 <option value="pickpocket">pickpocket</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
104 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
105 <expand macro="alleles" hla_regex="(HLA-[A-CEG]\*[0-8][[0-9]:[0-9][0-9][0-9]*|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-5]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
106 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
107 <help>Used for any alleles which don't include specified lengths</help>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
108 <option value="8" selected="true">8</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
109 <option value="9">9</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
110 <option value="10">10</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
111 <option value="11">11</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
112 <option value="12">12</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
113 <option value="13">13</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
114 <option value="14">14</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
115 <option value="15">15</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
116 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
117
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
118 </when>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
119 <when value="mhcii">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
120 <param name="method" type="select" label="prediction method">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
121 <option value="recommended" selected="true">recommended</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
122 <option value="consensus3">consensus3</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
123 <option value="NetMHCIIpan">NetMHCIIpan</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
124 <option value="nn_align">nn_align</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
125 <option value="smm_align">smm_align</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
126 <option value="comblib">comblib</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
127 <option value="tepitope">tepitope</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
128 </param>
4
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
129 <expand macro="alleles" hla_regex="(DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|(HLA-)?DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd])(,(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
130 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
131 <help>Used for any alleles which don't include specified lengths</help>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
132 <option value="asis">asis</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
133 <option value="11">11</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
134 <option value="12">12</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
135 <option value="13">13</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
136 <option value="14">14</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
137 <option value="15" selected="true">15</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
138 <option value="16">16</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
139 <option value="17">17</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
140 <option value="18">18</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
141 <option value="19">19</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
142 <option value="20">20</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
143 <option value="21">21</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
144 <option value="22">22</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
145 <option value="23">23</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
146 <option value="24">24</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
147 <option value="25">25</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
148 <option value="26">26</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
149 <option value="27">27</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
150 <option value="28">28</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
151 <option value="29">29</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
152 <option value="30">30</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
153 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
154 </when>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
155 <when value="processing">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
156 <param name="method" type="select" label="prediction method">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
157 <option value="recommended" selected="true">recommended</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
158 <option value="consensus">consensus</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
159 <option value="netmhcpan">netmhcpan</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
160 <option value="ann">ann</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
161 <option value="smmpmbec">smmpmbec</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
162 <option value="smm">smm</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
163 <option value="comblib_sidney2008">comblib_sidney2008</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
164 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
165 <param name="proteasome" type="select" label="proteasome type">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
166 <option value="immuno">immuno</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
167 <option value="constitutive">constitutive</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
168 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
169 <expand macro="alleles" hla_regex="(HLA-[A-CE]\*[0-8][[0-9]:[0-9][0-9]|BoLA-.+|Gogo-.+|H-2-[DKL][bdk]|Mamu-.+|Patr-.+|RT.+|SLA-.+)(,([8-9]|1[0-4]))*" hla_examples="HLA-A*03:01 HLA-B*07:02" hlalen_examples="HLA-A*03:01,8,9,10 HLA-B*07:02,9"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
170 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
171 <help>Used for any alleles which don't include specified lengths</help>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
172 <option value="8" selected="true">8</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
173 <option value="9">9</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
174 <option value="10">10</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
175 <option value="11">11</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
176 <option value="12">12</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
177 <option value="13">13</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
178 <option value="14">14</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
179 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
180 </when>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
181 <when value="mhcnp">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
182 <param name="method" type="select" label="prediction method">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
183 <option value="mhcnp" selected="true">mhcnp</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
184 <option value="netmhcpan">netmhcpan</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
185 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
186 <expand macro="alleles" hla_regex="(HLA-(A\*02:01|B\*07:02|B\*35:01|B\*44:03|B\*53:01|B\*57:01)|H-2-[DK]b)(,[8-9]|1[0-1])*" hla_examples="HLA-A*02:01 H-2-Db" hlalen_examples="HLA-A*02:01,8,9,10"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
187 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
188 <help>Used for any alleles which don't include specified lengths</help>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
189 <option value="8" selected="true">8</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
190 <option value="9">9</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
191 <option value="10">10</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
192 <option value="11">11</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
193 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
194 </when>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
195 <when value="bcell">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
196 <param name="method" type="select" label="prediction method">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
197 <option value="Bepipred" selected="true">Bepipred</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
198 <option value="Chou-Fasman">Chou-Fasman</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
199 <option value="Emini">Emini</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
200 <option value="Karplus-Schulz">Karplus-Schulz</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
201 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
202 <option value="Parker">Parker</option>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
203 </param>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
204 <param name="window_size" type="integer" value="" optional="true" min="1" label="window_size" help="window_size should be less than the sequence length, and less than 8 for Karplus-Schulz method"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
205 </when>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
206 </conditional>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
207 <conditional name="sequence">
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
208 <param name="seqsrc" type="select" label="Peptide sequences">
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
209 <option value="fasta">Fasta file</option>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
210 <option value="tabular">From tabular</option>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
211 <option value="entry"></option>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
212 </param>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
213 <when value="fasta">
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
214 <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
215 </when>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
216 <when value="tabular">
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
217 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
218 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" />
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
219 <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
220 </when>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
221 <when value="entry">
3
153d5fa7af53 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
jjohnson
parents: 2
diff changeset
222 <param name="seq_text" type="text" label="Peptide Sequence"/>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
223 </when>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
224 </conditional>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
225
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
226 </inputs>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
227 <outputs>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
228 <!--
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
229 <data name="output" format="tabular"/>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
230 -->
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
231 <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
232 <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
233 <filter>prediction['method'].startswith('Bepipred')</filter>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
234 </data>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
235 </outputs>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
236 <tests>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
237 <!-- test1 -->
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
238 <test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
239 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
240 <param name="tool" value="mhci"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
241 <param name="method" value="recommended"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
242 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
243 <param name="allelesrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
244 <param name="allele_text" value="HLA-A*01:01,9"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
245 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
246 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
247 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
248 <param name="seqsrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
249 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
250 </conditional>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
251 <output name="output">
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
252 <assert_contents>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
253 <has_text text="LYNTVATLY" />
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
254 </assert_contents>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
255 </output>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
256 </test>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
257 <!-- test2 -->
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
258 <test>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
259 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
260 <param name="tool" value="mhci"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
261 <param name="method" value="recommended"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
262 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
263 <param name="allelesrc" value="history"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
264 <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
265 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
266 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
267 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
268 <param name="seqsrc" value="fasta"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
269 <param name="seq_fasta" ftype="fasta" value="seqs.fa"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
270 </conditional>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
271 <output name="output">
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
272 <assert_contents>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
273 <has_text text="peptide1" />
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
274 <has_text text="HKVPRRLLK" />
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
275 </assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
276 </output>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
277 </test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
278 <!-- test3 -->
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
279 <test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
280 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
281 <param name="tool" value="mhci"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
282 <param name="method" value="recommended"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
283 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
284 <param name="allelesrc" value="history"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
285 <param name="allele_file" ftype="tabular" value="alleles.tsv"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
286 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
287 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
288 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
289 <param name="seqsrc" value="tabular"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
290 <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
291 <param name="pep_col" value="3"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
292 <param name="id_col" value="1"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
293 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
294 <output name="output">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
295 <assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
296 <has_text text="peptide1" />
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
297 <has_text text="HKVPRRLLK" />
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
298 </assert_contents>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
299 </output>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
300 </test>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
301 <!-- test4 -->
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
302 <test>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
303 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
304 <param name="tool" value="mhcii"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
305 <param name="method" value="recommended"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
306 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
307 <param name="allelesrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
308 <param name="allele_text" value="DPA1*01/DPB1*04:01"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
309 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
310 <param name="lengths" value="asis"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
311 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
312 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
313 <param name="seqsrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
314 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
315 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
316 <output name="output">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
317 <assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
318 <has_text text="LYNTVATLY" />
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
319 </assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
320 </output>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
321 </test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
322 <!-- test5 -->
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
323 <test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
324 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
325 <param name="tool" value="processing"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
326 <param name="method" value="recommended"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
327 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
328 <param name="allelesrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
329 <param name="allele_text" value="HLA-A*01:01,8 HLA-A*02:01,9"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
330 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
331 <param name="proteasome" value="constitutive"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
332 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
333 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
334 <param name="seqsrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
335 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
336 </conditional>
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
337 <output name="output">
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
338 <assert_contents>
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
339 <has_text text="LYNTVATLY" />
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
340 </assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
341 </output>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
342 </test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
343 <!-- test6 -->
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
344 <test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
345 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
346 <param name="tool" value="mhcnp"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
347 <param name="method" value="mhcnp"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
348 <conditional name="alleles">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
349 <param name="allelesrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
350 <param name="allele_text" value="HLA-A*02:01,9"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
351 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
352 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
353 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
354 <param name="seqsrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
355 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
356 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
357 <output name="output">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
358 <assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
359 <has_text text="LYNTVATLY" />
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
360 </assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
361 </output>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
362 </test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
363 <!-- test7 -->
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
364 <test>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
365 <conditional name="prediction">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
366 <param name="tool" value="bcell"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
367 <param name="method" value="Emini"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
368 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
369 <conditional name="sequence">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
370 <param name="seqsrc" value="entry"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
371 <param name="seq_text" value="VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTE"/>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
372 </conditional>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
373 <output name="output">
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
374 <assert_contents>
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
375 <has_text text="VLSEGE" />
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
376 </assert_contents>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
377 </output>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
378 </test>
4
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
379 <!-- test8 -->
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
380 <test>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
381 <conditional name="prediction">
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
382 <param name="tool" value="bcell"/>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
383 <param name="method" value="Bepipred"/>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
384 <param name="window_size" value="9"/>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
385 </conditional>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
386 <conditional name="sequence">
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
387 <param name="seqsrc" value="fasta"/>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
388 <param name="seq_fasta" ftype="fasta" value="bcell.fa"/>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
389 </conditional>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
390 <output name="output">
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
391 <assert_contents>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
392 <has_text text="ADVAGH" />
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
393 </assert_contents>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
394 </output>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
395 </test>
a14128950578 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 98a9dd3bd9c567e8b8e43ac5b54c4ba75a6fe78d"
jjohnson
parents: 3
diff changeset
396
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
397 </tests>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
398 <help><![CDATA[
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
399 The IEDB is a free resource, funded by a contract from the National Institute of Allergy and Infectious Diseases. It offers easy searching of experimental data characterizing antibody and T cell epitopes studied in humans, non-human primates, and other animal species.
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
400
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
401 This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB.
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
402 The webservices are described at: http://tools.immuneepitope.org/main/tools-api/
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
403 That page also describes how to retrieve the available HLA alleles for class of epitope binding.
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
404
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
405 **INPUTS**
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
406
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
407 peptide sequences from a fasta file or a column in a tabular file
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
408
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
409 HLA alleles either entered as text or one per line in a text file
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
410
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
411
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
412 **OUTPUTS**
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
413
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
414 A tabular file containing the results returned from the IEDB web service
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
415
2
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
416 **Typical Workflow for Human MHC I Binding Prediction**
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
417
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
418 The RNAseq data for the subject would be used for:
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
419
3
153d5fa7af53 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
jjohnson
parents: 2
diff changeset
420 - HLA prediction by seq2HLA
2
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
421 - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
422
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
423
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
424 .. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
425 :width: 584
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
426 :height: 430
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
427
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
428 .. note:: The seq2HLA ClassI.HLAgenotype4digits output needs to be converted for IEDB alleles.
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
429
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
430 The seq2HLA ClassI.HLAgenotype4digits output:
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
431
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
432 .. image:: $PATH_TO_IMAGES/seq2HLA_ClassI.HLAgenotype4digits.png
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
433 :width: 285
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
434 :height: 77
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
435
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
436 Needs to be converted into IEDB formatted alleles:
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
437
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
438 .. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
439 :width: 74
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
440 :height: 81
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
441
3
153d5fa7af53 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
jjohnson
parents: 2
diff changeset
442 In the workflow above QueryTabular tool converts the alleles:
2
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
443
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
444 - Filter Dataset Input
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
445
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
446 * skip leading lines - *skip lines:* 1
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
447 * select columns - *columns:* 2,4
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
448 * regex replace value in column - *column:* 1 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
449 * regex replace value in column - *column:* 2 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
450
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
451 - SQL Query to generate tabular output
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
452
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
453 * SELECT c1 FROM t1 UNION SELECT c2 FROM t1
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
454
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
455
3
153d5fa7af53 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
jjohnson
parents: 2
diff changeset
456 The IEDB formatting can also be performed by TextProcessing tools:
2
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
457
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
458 .. image:: $PATH_TO_IMAGES/TextProcessingConversion.png
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
459 :width: 608
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
460 :height: 87
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
461
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
462 The TextProcessing steps to convert the alleles:
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
463
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
464 - Remove beginning - removes the header line
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
465 - Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
466
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
467 * *Find pattern:* ^.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*$
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
468 * *Replace with:* HLA-\\1\\nHLA-\\2
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
469
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
470 - Unique - remove duplicates
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
471
883cdf0ffae5 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
jjohnson
parents: 1
diff changeset
472
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
473 ]]></help>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
474 <citations>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
475 <citation type="doi">10.1093/nar/gku938</citation>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
476 </citations>
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
477 </tool>