Mercurial > repos > jjohnson > iedb_api
annotate iedb_api.xml @ 2:883cdf0ffae5 draft
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
author | jjohnson |
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date | Wed, 26 Feb 2020 15:02:37 -0500 |
parents | 4a89ba6cfc63 |
children | 153d5fa7af53 |
rev | line source |
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1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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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
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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
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3 <macros> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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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:
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5 <conditional name="alleles"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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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
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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:
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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:
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9 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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10 <when value="history"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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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
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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:
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13 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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14 </when> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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15 <when value="entry"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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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:
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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:
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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:
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19 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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20 </when> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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21 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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22 </xml> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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23 </macros> |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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24 <requirements> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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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
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26 </requirements> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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27 <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
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28 #import re |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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29 python '${__tool_directory__}/iedb_api.py' |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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30 --prediction=$prediction.tool |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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31 --method=$prediction.method |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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32 #if $prediction.tool == 'bcell': |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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33 #if $prediction.window_size: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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34 -w $prediction.window_size |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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35 #end if |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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36 #else |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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37 #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
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38 --proteasome $prediction.proteasome |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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39 #end if |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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40 #if $prediction.alleles.allelesrc == 'history': |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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41 #for $line in open(str($prediction.alleles.allele_file)): |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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42 #set $fields = $line.strip().split(',') |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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43 #set $allele = $fields[0].strip() |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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44 #if len($allele) > 0: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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45 #if len($fields) > 1: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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46 #for $alen in $fields[1:]: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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47 -a '$allele' -l $alen |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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48 #end for |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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49 #else: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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50 #for $alen in str($prediction.lengths).split(','): |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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51 -a '$allele' -l $alen |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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52 #end for |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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53 #end if |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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54 #end if |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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55 #end for |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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56 #else: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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57 #for $word in str($prediction.alleles.allele_text).strip().split(): |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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58 #set $fields = $word.strip().split(',') |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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59 #set $allele = $fields[0].strip() |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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60 #if len($allele) > 0: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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61 #if len($fields) > 1: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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62 #for $alen in $fields[1:]: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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63 -a '$allele' -l $alen |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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64 #end for |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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65 #else: |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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66 #for $alen in str($prediction.lengths).split(','): |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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67 -a '$allele' -l $alen |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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68 #end for |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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69 #end if |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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70 #end if |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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71 #end for |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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72 #end if |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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73 #end if |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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74 |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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75 #if $sequence.seqsrc == 'fasta': |
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4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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76 -i '$sequence.seq_fasta' |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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77 #else if $sequence.seqsrc == 'tabular': |
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4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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78 -i '$sequence.seq_tsv' |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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79 -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
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80 #if $sequence.id_col: |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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81 -C #echo int(str($sequence.id_col)) - 1 |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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82 #end if |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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83 #else: |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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84 #for $seq in str($sequence.seq_text).strip().split(): |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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85 -s $seq.strip() |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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86 #end for |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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87 #end if |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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88 -o $output |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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89 ]]></command> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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90 <inputs> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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91 <conditional name="prediction"> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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92 <param name="tool" type="select" label="Prediction"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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93 <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:
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94 <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:
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95 <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:
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96 <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
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97 <option value="bcell">Antibody Epitope Prediction</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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98 </param> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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99 <when value="mhci"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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100 <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"
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101 <option value="recommended" selected="true">recommended</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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102 <option value="consensus">consensus</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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103 <option value="netmhcpan">netmhcpan</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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104 <option value="ann">ann</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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105 <option value="smmpmbec">smmpmbec</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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106 <option value="smm">smm</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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107 <option value="comblib_sidney2008">comblib_sidney2008</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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108 <option value="netmhccons">netmhccons</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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109 <option value="pickpocket">pickpocket</option> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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110 </param> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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111 <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"
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112 <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"
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113 <help>Used for any alleles which don't include specified lengths</help> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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114 <option value="8" selected="true">8</option> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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115 <option value="9">9</option> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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116 <option value="10">10</option> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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117 <option value="11">11</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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118 <option value="12">12</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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119 <option value="13">13</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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120 <option value="14">14</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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121 <option value="15">15</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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122 </param> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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123 |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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124 </when> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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125 <when value="mhcii"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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126 <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
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127 <option value="recommended" selected="true">recommended</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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128 <option value="consensus3">consensus3</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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129 <option value="NetMHCIIpan">NetMHCIIpan</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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130 <option value="nn_align">nn_align</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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131 <option value="smm_align">smm_align</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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132 <option value="comblib">comblib</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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133 <option value="tepitope">tepitope</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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134 </param> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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135 <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]|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"/> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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136 <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"
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137 <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"
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138 <option value="asis">asis</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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139 <option value="11">11</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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140 <option value="12">12</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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141 <option value="13">13</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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142 <option value="14">14</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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143 <option value="15" selected="true">15</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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144 <option value="16">16</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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145 <option value="17">17</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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146 <option value="18">18</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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147 <option value="19">19</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
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148 <option value="20">20</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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149 <option value="21">21</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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150 <option value="22">22</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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151 <option value="23">23</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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152 <option value="24">24</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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153 <option value="25">25</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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154 <option value="26">26</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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155 <option value="27">27</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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156 <option value="28">28</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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0
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157 <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
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158 <option value="30">30</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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159 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
160 </when> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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161 <when value="processing"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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|
162 <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:
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163 <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:
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164 <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
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165 <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
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166 <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
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167 <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
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168 <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
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169 <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
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170 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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171 <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:
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172 <option value="immuno">immuno</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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173 <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
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|
174 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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|
175 <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:
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|
176 <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:
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177 <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:
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178 <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
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179 <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
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180 <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
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181 <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
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182 <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
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|
183 <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
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184 <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
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185 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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186 </when> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
187 <when value="mhcnp"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
188 <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
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189 <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
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|
190 <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
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191 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
192 <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
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193 <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:
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194 <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
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195 <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
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196 <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
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197 <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
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198 <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
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199 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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200 </when> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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201 <when value="bcell"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
202 <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
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203 <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
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204 <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
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205 <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
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|
206 <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
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|
207 <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
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208 <option value="Parker">Parker</option> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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209 </param> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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210 <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
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211 </when> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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212 </conditional> |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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213 <conditional name="sequence"> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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214 <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:
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215 <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:
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216 <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:
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217 <option value="entry"></option> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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218 </param> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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219 <when value="fasta"> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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220 <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:
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221 </when> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
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222 <when value="tabular"> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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|
223 <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:
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|
224 <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:
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|
225 <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:
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226 </when> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
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227 <when value="entry"> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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228 <param name="seq_text" type="text" size="80" label="Peptide Sequence"/> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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229 </when> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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230 </conditional> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
231 |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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232 </inputs> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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233 <outputs> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
234 <!-- |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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|
235 <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
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236 --> |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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|
237 <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
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|
238 <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
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239 <filter>prediction['method'].startswith('Bepipred')</filter> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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240 </data> |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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241 </outputs> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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242 <tests> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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0
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|
243 <!-- test1 --> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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0
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244 <test> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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245 <conditional name="prediction"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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246 <param name="tool" value="mhci"/> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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247 <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
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|
248 <conditional name="alleles"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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249 <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
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|
250 <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
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|
251 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
252 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
253 <conditional name="sequence"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
254 <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
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255 <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
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|
256 </conditional> |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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257 <output name="output"> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
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258 <assert_contents> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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259 <has_text text="LYNTVATLY" /> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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260 </assert_contents> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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261 </output> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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|
262 </test> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
263 <!-- test2 --> |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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diff
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264 <test> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
265 <conditional name="prediction"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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266 <param name="tool" value="mhci"/> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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267 <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
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|
268 <conditional name="alleles"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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|
269 <param name="allelesrc" value="history"/> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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|
270 <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
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0
diff
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|
271 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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0
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|
272 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
273 <conditional name="sequence"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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274 <param name="seqsrc" value="fasta"/> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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275 <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
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0
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|
276 </conditional> |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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277 <output name="output"> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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278 <assert_contents> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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279 <has_text text="peptide1" /> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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|
280 <has_text text="HKVPRRLLK" /> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
281 </assert_contents> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
282 </output> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
283 </test> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
284 <!-- test3 --> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
285 <test> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
286 <conditional name="prediction"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
287 <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
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|
288 <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
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|
289 <conditional name="alleles"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
290 <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
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|
291 <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
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|
292 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
293 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
294 <conditional name="sequence"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
295 <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
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|
296 <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
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|
297 <param name="pep_col" value="3"/> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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298 <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
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|
299 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
300 <output name="output"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
301 <assert_contents> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
302 <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
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|
303 <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
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|
304 </assert_contents> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
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|
305 </output> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
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|
306 </test> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
307 <!-- test4 --> |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
308 <test> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
309 <conditional name="prediction"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
310 <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
|
311 <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
|
312 <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
|
313 <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
|
314 <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
|
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 <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
|
317 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
318 <conditional name="sequence"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
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|
319 <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
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|
320 <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
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|
321 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
322 <output name="output"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
323 <assert_contents> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
324 <has_text text="LYNTVATLY" /> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
325 </assert_contents> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
326 </output> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
327 </test> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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|
328 <!-- test5 --> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
329 <test> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
330 <conditional name="prediction"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
331 <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
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|
332 <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
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|
333 <conditional name="alleles"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
334 <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
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|
335 <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
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|
336 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
337 <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
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|
338 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
339 <conditional name="sequence"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
340 <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
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|
341 <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
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|
342 </conditional> |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
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343 <output name="output"> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
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344 <assert_contents> |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
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|
345 <has_text text="LYNTVATLY" /> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
346 </assert_contents> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
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|
347 </output> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
348 </test> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
349 <!-- test6 --> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
350 <test> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
351 <conditional name="prediction"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
352 <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
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|
353 <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
|
354 <conditional name="alleles"> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
355 <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
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|
356 <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
|
357 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
358 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
359 <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
|
360 <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
|
361 <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
|
362 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
363 <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
|
364 <assert_contents> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
365 <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
|
366 </assert_contents> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
367 </output> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
368 </test> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
369 <!-- test7 --> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
370 <test> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
371 <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
|
372 <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
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|
373 <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
|
374 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
375 <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
|
376 <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
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|
377 <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
|
378 </conditional> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
379 <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
|
380 <assert_contents> |
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
381 <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
|
382 </assert_contents> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
383 </output> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
384 </test> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
385 </tests> |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
386 <help><![CDATA[ |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
387 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
|
388 |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
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|
389 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
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|
390 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
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|
391 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
|
392 |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
393 **INPUTS** |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
394 |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
395 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
|
396 |
1
4a89ba6cfc63
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents:
0
diff
changeset
|
397 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
|
398 |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
399 |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
400 **OUTPUTS** |
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff
changeset
|
401 |
991424605492
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402 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"
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403 |
2
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404 **Typical Workflow for Human MHC I Binding Prediction** |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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405 |
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406 The RNAseq data for the subject would be used for: |
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407 |
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408 - HLA prediction by seq2HLA_ |
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409 - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta |
883cdf0ffae5
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410 |
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411 .. _seq2HLA: https://toolshed.g2.bx.psu.edu/view/iuc/seq2hla/52bba1cd3823 |
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412 |
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413 .. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png |
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414 :width: 584 |
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415 :height: 430 |
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416 |
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417 .. note:: The seq2HLA ClassI.HLAgenotype4digits output needs to be converted for IEDB alleles. |
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418 |
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419 The seq2HLA ClassI.HLAgenotype4digits output: |
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420 |
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421 .. image:: $PATH_TO_IMAGES/seq2HLA_ClassI.HLAgenotype4digits.png |
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422 :width: 285 |
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423 :height: 77 |
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424 |
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425 Needs to be converted into IEDB formatted alleles: |
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426 |
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427 .. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png |
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428 :width: 74 |
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429 :height: 81 |
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430 |
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431 In the workflow above QueryTabular_ tool converts the alleles: |
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432 |
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433 - Filter Dataset Input |
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434 |
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435 * skip leading lines - *skip lines:* 1 |
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436 * select columns - *columns:* 2,4 |
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437 * regex replace value in column - *column:* 1 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 |
883cdf0ffae5
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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438 * regex replace value in column - *column:* 2 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 |
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439 |
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440 - SQL Query to generate tabular output |
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441 |
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442 * SELECT c1 FROM t1 UNION SELECT c2 FROM t1 |
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443 |
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444 .. _QueryTabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/0c95a3f1654f |
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445 |
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446 |
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447 The IEDB formatting can also be performed by TextProcessing_ tools: |
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448 |
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449 .. _TextProcessing: https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing/0a8c6b61f0f4 |
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450 |
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451 .. image:: $PATH_TO_IMAGES/TextProcessingConversion.png |
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452 :width: 608 |
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453 :height: 87 |
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454 |
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455 The TextProcessing steps to convert the alleles: |
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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 8e90bc55d0f086038b1665521fd992bed7aaa8ca"
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456 |
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457 - Remove beginning - removes the header line |
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458 - Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line |
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459 |
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460 * *Find pattern:* ^.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*\\t([a-zA-Z]+[*][0-9]{2}:[0-9]{2,3}).*\\t.*$ |
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461 * *Replace with:* HLA-\\1\\nHLA-\\2 |
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462 |
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463 - Unique - remove duplicates |
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464 |
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465 |
0
991424605492
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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466 ]]></help> |
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467 <citations> |
991424605492
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468 <citation type="doi">10.1093/nar/gku938</citation> |
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469 </citations> |
991424605492
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470 </tool> |