Mercurial > repos > iuc > iedb_api
annotate iedb_api.xml @ 3:e95d3221b7f0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 863578373c7dadc5880633115b0c348f73dac782"
author | iuc |
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date | Fri, 11 Sep 2020 21:02:34 +0000 |
parents | a09849898387 |
children | 7ed6dda64a81 |
rev | line source |
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3
e95d3221b7f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 863578373c7dadc5880633115b0c348f73dac782"
iuc
parents:
2
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1 <tool id="iedb_api" name="IEDB" version="2.15.1"> |
0
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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2 <description>MHC Binding prediction</description> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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3 <macros> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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4 <xml name="alleles" token_hla_regex="" token_hla_examples="" token_hlalen_examples=""> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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5 <conditional name="alleles"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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6 <param name="allelesrc" type="select" label="Alleles"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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7 <option value="history">From history</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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8 <option value="entry">Entered</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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9 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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10 <when value="history"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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11 <param name="allele_file" type="data" format="txt" label="Alleles file"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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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> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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13 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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14 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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15 <when value="entry"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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16 <param name="allele_text" type="text" size="80" label="Alleles"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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18 <validator type="regex" message="Doesn't appear to be a valid allele">^@HLA_REGEX@(\s+@HLA_REGEX@)*$</validator> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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19 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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20 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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21 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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22 </xml> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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23 </macros> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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24 <requirements> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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25 <requirement type="package" version="3.7">python</requirement> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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26 </requirements> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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27 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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28 <command detect_errors="exit_code"><![CDATA[ |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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29 #import re |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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30 python '${__tool_directory__}/iedb_api.py' |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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31 --prediction=$prediction.tool |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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32 --method=$prediction.method |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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33 #if $prediction.tool == 'bcell': |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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34 #if $prediction.window_size: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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35 -w $prediction.window_size |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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36 #end if |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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37 #else |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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38 #if $prediction.tool == 'processing' and $prediction.proteasome: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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39 --proteasome $prediction.proteasome |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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40 #end if |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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41 #if $prediction.alleles.allelesrc == 'history': |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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42 -A '$prediction.alleles.allele_file' |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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43 #else: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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44 -A '$entered_alleles' |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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45 #end if |
3
e95d3221b7f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 863578373c7dadc5880633115b0c348f73dac782"
iuc
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46 -l '$prediction.lengths' |
0
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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47 #end if |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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48 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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49 #if $sequence.seqsrc == 'fasta': |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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50 -i '$sequence.seq_fasta' |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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51 #else if $sequence.seqsrc == 'tabular': |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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52 -i '$sequence.seq_tsv' |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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53 -c #echo int(str($sequence.pep_col)) - 1 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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54 #if $sequence.id_col: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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55 -C #echo int(str($sequence.id_col)) - 1 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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56 #end if |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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57 #else: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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58 -i '$entered_seqs' -c 1 -C 0 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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59 #end if |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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60 -o '$output' |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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61 ]]></command> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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62 <configfiles> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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63 <configfile name="entered_alleles"><![CDATA[#slurp |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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64 #if $prediction.tool != 'bcell' and $prediction.alleles.allelesrc == 'entry' |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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65 #for $word in str($prediction.alleles.allele_text).strip().split(): |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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66 #if $word.find(',') > 0 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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67 $word |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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68 #else |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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69 #set $allele = $word + ',' + str($prediction.lengths) |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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70 $allele |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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71 #end if |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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72 #end for |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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73 #end if |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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74 ]]></configfile> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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75 <configfile name="entered_seqs"><![CDATA[#slurp |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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76 #if $sequence.seqsrc == 'entry' |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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77 #for $i, $seq in enumerate(str($sequence.seq_text).strip().split()) |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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78 #set $seqid = $i + 1 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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79 #set $seqtext = '\t'.join([str($seqid),$seq.strip()]) |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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80 $seqtext |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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81 #end for |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
82 #end if |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
83 ]]></configfile> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
84 </configfiles> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
85 <inputs> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
86 <conditional name="prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
87 <param name="tool" type="select" label="Prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
88 <option value="mhci">MHC-I Binding</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
89 <option value="mhcii">MHC-II Binding</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
90 <option value="processing">MHC-I Processing</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
91 <option value="mhcnp">MHC-NP T-Cell Epitope</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
92 <option value="bcell">Antibody Epitope Prediction</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
93 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
94 <when value="mhci"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
95 <param name="method" type="select" label="prediction method"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
96 <option value="recommended" selected="true">recommended</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
97 <option value="consensus">consensus</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
98 <option value="netmhcpan">netmhcpan</option> |
3
e95d3221b7f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 863578373c7dadc5880633115b0c348f73dac782"
iuc
parents:
2
diff
changeset
|
99 <option value="netmhcpan_ba">netmhcpan_ba</option> |
e95d3221b7f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 863578373c7dadc5880633115b0c348f73dac782"
iuc
parents:
2
diff
changeset
|
100 <option value="netmhcpan_el">netmhcpan_el</option> |
0
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
101 <option value="ann">ann</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
102 <option value="smmpmbec">smmpmbec</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
103 <option value="smm">smm</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
104 <option value="comblib_sidney2008">comblib_sidney2008</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
105 <option value="netmhccons">netmhccons</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
106 <option value="pickpocket">pickpocket</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
107 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
108 <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"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
109 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
110 <help>Used for any alleles which don't include specified lengths</help> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
111 <option value="8" selected="true">8</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
112 <option value="9">9</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
113 <option value="10">10</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
114 <option value="11">11</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
115 <option value="12">12</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
116 <option value="13">13</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
117 <option value="14">14</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
118 <option value="15">15</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
119 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
120 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
121 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
122 <when value="mhcii"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
123 <param name="method" type="select" label="prediction method"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
124 <option value="recommended" selected="true">recommended</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
125 <option value="consensus3">consensus3</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
126 <option value="NetMHCIIpan">NetMHCIIpan</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
127 <option value="nn_align">nn_align</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
128 <option value="smm_align">smm_align</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
129 <option value="comblib">comblib</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
130 <option value="tepitope">tepitope</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
131 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
132 <expand macro="alleles" hla_regex="(DPA1\*0[1-3](:0[1-3])?/DPB1\*0[1-6]:0[12]|DQA1\*0[1-5]:0[12]/DQB1\*0[2-6]:0[12]|(HLA-)?DRB[1-5]\*[01][1-9]:0[1-5]|H2-IA[bd])(,(asis|[1-2][0-9]|30))*" hla_examples="DPA1*01/DPB1*04:01 HLA-DRB1*01:01 H2-IAb" hlalen_examples="DPA1*01/DPB1*04:01,11,15"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
133 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
134 <help>Used for any alleles which don't include specified lengths</help> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
135 <option value="asis">asis</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
136 <option value="11">11</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
137 <option value="12">12</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
138 <option value="13">13</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
139 <option value="14">14</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
140 <option value="15" selected="true">15</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
141 <option value="16">16</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
142 <option value="17">17</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
143 <option value="18">18</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
144 <option value="19">19</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
145 <option value="20">20</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
146 <option value="21">21</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
147 <option value="22">22</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
148 <option value="23">23</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
149 <option value="24">24</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
150 <option value="25">25</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
151 <option value="26">26</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
152 <option value="27">27</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
153 <option value="28">28</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
154 <option value="29">29</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
155 <option value="30">30</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
156 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
157 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
158 <when value="processing"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
159 <param name="method" type="select" label="prediction method"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
160 <option value="recommended" selected="true">recommended</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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161 <option value="consensus">consensus</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
162 <option value="netmhcpan">netmhcpan</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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163 <option value="ann">ann</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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164 <option value="smmpmbec">smmpmbec</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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165 <option value="smm">smm</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
166 <option value="comblib_sidney2008">comblib_sidney2008</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
167 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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168 <param name="proteasome" type="select" label="proteasome type"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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169 <option value="immuno">immuno</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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170 <option value="constitutive">constitutive</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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171 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
172 <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"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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173 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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174 <help>Used for any alleles which don't include specified lengths</help> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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175 <option value="8" selected="true">8</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
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176 <option value="9">9</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
177 <option value="10">10</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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178 <option value="11">11</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
179 <option value="12">12</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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180 <option value="13">13</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
181 <option value="14">14</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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182 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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183 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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184 <when value="mhcnp"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
185 <param name="method" type="select" label="prediction method"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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186 <option value="mhcnp" selected="true">mhcnp</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
187 <option value="netmhcpan">netmhcpan</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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188 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
189 <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"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
190 <param name="lengths" type="select" multiple="true" optional="false" label="peptide lengths for prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
191 <help>Used for any alleles which don't include specified lengths</help> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
192 <option value="8" selected="true">8</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
193 <option value="9">9</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
194 <option value="10">10</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
195 <option value="11">11</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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196 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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197 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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198 <when value="bcell"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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199 <param name="method" type="select" label="prediction method"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
200 <option value="Bepipred" selected="true">Bepipred</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
201 <option value="Chou-Fasman">Chou-Fasman</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
202 <option value="Emini">Emini</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
203 <option value="Karplus-Schulz">Karplus-Schulz</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
204 <option value="Kolaskar-Tongaonkar">Kolaskar-Tongaonkar</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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205 <option value="Parker">Parker</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
206 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
207 <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"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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208 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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209 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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210 <conditional name="sequence"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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211 <param name="seqsrc" type="select" label="Peptide sequences"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
212 <option value="fasta">Fasta file</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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213 <option value="tabular">From tabular</option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
214 <option value="entry"></option> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
215 </param> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
216 <when value="fasta"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
217 <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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218 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
219 <when value="tabular"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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220 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
221 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
222 <param name="id_col" label="Select column with name" type="data_column" numerical="false" data_ref="seq_tsv" optional="true"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
223 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
224 <when value="entry"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
225 <param name="seq_text" type="text" label="Peptide Sequence"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
226 </when> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
227 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
228 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
229 </inputs> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
230 <outputs> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
231 <!-- |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
232 <data name="output" format="tabular"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
233 --> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
234 <data name="output" format="tabular" label="IEDB ${prediction.tool} ${prediction.method}"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
235 <data name="output2" format="tabular" label="IEDB ${prediction.tool} ${prediction.method} residue scores" from_work_dir="iedb_results2"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
236 <filter>prediction['method'].startswith('Bepipred')</filter> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
237 </data> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
238 </outputs> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
239 <tests> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
240 <!-- test1 --> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
241 <test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
242 <conditional name="prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
243 <param name="tool" value="mhci"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
244 <param name="method" value="recommended"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
245 <conditional name="alleles"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
246 <param name="allelesrc" value="entry"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
247 <param name="allele_text" value="HLA-A*01:01,9"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
248 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
249 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
250 <conditional name="sequence"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
251 <param name="seqsrc" value="entry"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
252 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
253 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
254 <output name="output"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
255 <assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
256 <has_text text="LYNTVATLY" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
257 </assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
258 </output> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
259 </test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
260 <!-- test2 --> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
261 <test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
262 <conditional name="prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
263 <param name="tool" value="mhci"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
264 <param name="method" value="recommended"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
265 <conditional name="alleles"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
266 <param name="allelesrc" value="history"/> |
3
e95d3221b7f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 863578373c7dadc5880633115b0c348f73dac782"
iuc
parents:
2
diff
changeset
|
267 <param name="allele_file" ftype="tabular" value="alleles_len.tsv"/> |
0
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
268 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
269 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
270 <conditional name="sequence"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
271 <param name="seqsrc" value="fasta"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
272 <param name="seq_fasta" ftype="fasta" value="seqs.fa"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
273 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
274 <output name="output"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
275 <assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
276 <has_text text="peptide1" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
277 <has_text text="HKVPRRLLK" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
278 </assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
279 </output> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
280 </test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
281 <!-- test3 --> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
282 <test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
283 <conditional name="prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
284 <param name="tool" value="mhci"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
285 <param name="method" value="recommended"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
286 <conditional name="alleles"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
287 <param name="allelesrc" value="history"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
288 <param name="allele_file" ftype="tabular" value="alleles.tsv"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
289 </conditional> |
3
e95d3221b7f0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 863578373c7dadc5880633115b0c348f73dac782"
iuc
parents:
2
diff
changeset
|
290 <param name="lengths" value="8,9"/> |
0
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
291 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
292 <conditional name="sequence"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
293 <param name="seqsrc" value="tabular"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
294 <param name="seq_tsv" ftype="tabular" value="seqs.tsv"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
295 <param name="pep_col" value="3"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
296 <param name="id_col" value="1"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
297 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
298 <output name="output"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
299 <assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
300 <has_text text="peptide1" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
301 <has_text text="HKVPRRLLK" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
302 </assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
303 </output> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
304 </test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
305 <!-- test4 --> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
306 <test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
307 <conditional name="prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
308 <param name="tool" value="mhcii"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
309 <param name="method" value="recommended"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
310 <conditional name="alleles"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
311 <param name="allelesrc" value="entry"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
312 <param name="allele_text" value="DPA1*01/DPB1*04:01"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
313 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
314 <param name="lengths" value="asis"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
315 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
316 <conditional name="sequence"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
317 <param name="seqsrc" value="entry"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
318 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
319 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
320 <output name="output"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
321 <assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
322 <has_text text="LYNTVATLY" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
323 </assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
324 </output> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
325 </test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
326 <!-- test5 --> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
327 <test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
328 <conditional name="prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
329 <param name="tool" value="processing"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
330 <param name="method" value="recommended"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
331 <conditional name="alleles"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
332 <param name="allelesrc" value="entry"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
333 <param name="allele_text" value="HLA-A*01:01,8 HLA-A*02:01,9"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
334 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
335 <param name="proteasome" value="constitutive"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
336 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
337 <conditional name="sequence"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
338 <param name="seqsrc" value="entry"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
339 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
340 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
341 <output name="output"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
342 <assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
343 <has_text text="LYNTVATLY" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
344 </assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
345 </output> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
346 </test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
347 <!-- test6 --> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
348 <test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
349 <conditional name="prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
350 <param name="tool" value="mhcnp"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
351 <param name="method" value="mhcnp"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
352 <conditional name="alleles"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
353 <param name="allelesrc" value="entry"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
354 <param name="allele_text" value="HLA-A*02:01,9"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
355 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
356 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
357 <conditional name="sequence"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
358 <param name="seqsrc" value="entry"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
359 <param name="seq_text" value="SLYNTVATLYCVHQRIDV"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
360 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
361 <output name="output"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
362 <assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
363 <has_text text="LYNTVATLY" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
364 </assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
365 </output> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
366 </test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
367 <!-- test7 --> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
368 <test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
369 <conditional name="prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
370 <param name="tool" value="bcell"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
371 <param name="method" value="Emini"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
372 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
373 <conditional name="sequence"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
374 <param name="seqsrc" value="entry"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
375 <param name="seq_text" value="VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTE"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
376 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
377 <output name="output"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
378 <assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
379 <has_text text="VLSEGE" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
380 </assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
381 </output> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
382 </test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
383 <!-- test8 --> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
384 <test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
385 <conditional name="prediction"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
386 <param name="tool" value="bcell"/> |
2
a09849898387
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit f4629adca2e0f6d5f0cdfea8e11ce65abf218adf"
iuc
parents:
0
diff
changeset
|
387 <param name="method" value="Kolaskar-Tongaonkar"/> |
0
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
388 <param name="window_size" value="9"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
389 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
390 <conditional name="sequence"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
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|
391 <param name="seqsrc" value="fasta"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
392 <param name="seq_fasta" ftype="fasta" value="bcell.fa"/> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
393 </conditional> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
394 <output name="output"> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
395 <assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
396 <has_text text="ADVAGH" /> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
397 </assert_contents> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
398 </output> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
399 </test> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
400 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
401 </tests> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
402 <help><![CDATA[ |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
403 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. |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
404 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
405 This tool retrieves epitope binding information about input peptide sequences by using the RESTful web services provided by IEDB. |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
406 The webservices are described at: http://tools.immuneepitope.org/main/tools-api/ |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff
changeset
|
407 That page also describes how to retrieve the available HLA alleles for class of epitope binding. |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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408 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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409 **INPUTS** |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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410 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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411 peptide sequences from a fasta file or a column in a tabular file |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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412 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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413 HLA alleles either entered as text or one per line in a text file |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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414 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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415 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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416 **OUTPUTS** |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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417 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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418 A tabular file containing the results returned from the IEDB web service |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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419 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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420 **Typical Workflow for Human MHC I Binding Prediction** |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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421 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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422 The RNAseq data for the subject would be used for: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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423 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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424 - HLA prediction by seq2HLA |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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425 - Novel Antigen Prediction by a variety of workflows to generate a Antigen peptide fasta |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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426 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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427 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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428 .. image:: $PATH_TO_IMAGES/IEDB_Workflow_QueryTabular.png |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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429 :width: 584 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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430 :height: 430 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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431 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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432 .. note:: The seq2HLA ClassI.HLAgenotype4digits output needs to be converted for IEDB alleles. |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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433 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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434 The seq2HLA ClassI.HLAgenotype4digits output: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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435 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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436 .. image:: $PATH_TO_IMAGES/seq2HLA_ClassI.HLAgenotype4digits.png |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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437 :width: 285 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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438 :height: 77 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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439 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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440 Needs to be converted into IEDB formatted alleles: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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441 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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442 .. image:: $PATH_TO_IMAGES/IEDB_formatted_alleles.png |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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443 :width: 74 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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444 :height: 81 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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445 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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446 In the workflow above QueryTabular tool converts the alleles: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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447 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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448 - Filter Dataset Input |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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449 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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450 * skip leading lines - *skip lines:* 1 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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451 * select columns - *columns:* 2,4 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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452 * regex replace value in column - *column:* 1 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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453 * regex replace value in column - *column:* 2 *regex pattern:* ^(\\w+[*]\\d\\d:\\d\\d\\d?).*$ *replacement expression:* HLA-\\1 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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454 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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455 - SQL Query to generate tabular output |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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456 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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457 * SELECT c1 FROM t1 UNION SELECT c2 FROM t1 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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458 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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459 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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460 The IEDB formatting can also be performed by TextProcessing tools: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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461 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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462 .. image:: $PATH_TO_IMAGES/TextProcessingConversion.png |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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463 :width: 608 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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464 :height: 87 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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465 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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466 The TextProcessing steps to convert the alleles: |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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467 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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468 - Remove beginning - removes the header line |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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469 - Replace Text - picks Allele 1 and Allele 2 from each line and reformats each on a separate line |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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470 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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471 * *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.*$ |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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472 * *Replace with:* HLA-\\1\\nHLA-\\2 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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473 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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474 - Unique - remove duplicates |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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475 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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476 |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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477 ]]></help> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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|
478 <citations> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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479 <citation type="doi">10.1093/nar/gku938</citation> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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480 </citations> |
fe3c43451319
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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481 </tool> |