Mercurial > repos > galaxyp > iedb_netmhcpan

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
author galaxyp
date Wed, 09 Jul 2025 12:56:30 +0000
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88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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1 <macros>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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2 <xml name="requirements">
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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3 <requirement type="package" version="3.13">python</requirement>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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4 </xml>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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5 <xml name="configfiles">
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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6 <configfile name="entered_alleles"><![CDATA[#slurp
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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7 #if $alleles.allelesrc == 'entry'
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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8 #if $alleles.allele_text != ''
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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9 #for $allele in str($alleles.allele_text).strip().split():
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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10 $allele
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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11 #end for
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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12 #end if
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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13 #if $alleles.allele_select != 'None'
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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14 #for $allele in $alleles.allele_select:
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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15 $allele
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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16 #end for
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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17 #end if
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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18 #end if
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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19 ]]></configfile>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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20 <configfile name="entered_seqs"><![CDATA[#slurp
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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21 #if $sequence.seqsrc == 'entry'
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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22 #for $seq in str($sequence.seq_text).strip().split()
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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23 $seq
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24 #end for
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25 #end if
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26 ]]></configfile>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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27 </xml>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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28 <xml name="inputs" token_hla_regex="" token_hla_examples="" token_hlalen_examples="">
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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29 <conditional name="alleles">
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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30 <param name="allelesrc" type="select" label="Alleles">
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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31 <option value="history">From history</option>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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32 <option value="entry">Entered</option>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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33 </param>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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34 <when value="history">
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35 <param name="allele_file" type="data" format="txt" label="Alleles file">
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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36 <help>The dataset should have one allele per line. The allele may be followed by an optional comma-separated list of peptide lengths, e.g.: @HLALEN_EXAMPLES@</help>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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37 </param>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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38 </when>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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39 <when value="entry">
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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40 <param name="allele_text" type="text" label="Alleles" optional="true">
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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41 <help>Enter alleles separated by white space: @HLA_EXAMPLES@ (The peptide lengths may follow each allele: @HLALEN_EXAMPLES@)</help>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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42 </param>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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43 <expand macro="allele_list_macro" />
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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44 </when>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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45 </conditional>
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46 <param name="length_start" type="integer" optional="false" value="8" label="Peptide length range start"/>
88e44dab2988 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/iedb_netmhcpan commit 0ac7534c8d9f5bfea21b998286f822784e62da08
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47 <param name="length_end" type="integer" optional="false" value="8" label="Peptide length range end"/>
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48 <conditional name="sequence">
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49 <param name="seqsrc" type="select" label="Peptide sequences">
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50 <option value="fasta">Fasta file</option>
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51 <option value="tabular">From tabular</option>
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52 <option value="entry">Enter sequences</option>
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53 </param>
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54 <when value="fasta">
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55 <param name="seq_fasta" type="data" format="fasta" label="Peptide Sequence Fasta"/>
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56 </when>
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57 <when value="tabular">
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58 <param name="seq_tsv" type="data" format="tabular" label="Peptide Sequence Tabular"/>
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59 <param name="pep_col" label="Select column with peptides" type="data_column" numerical="false" data_ref="seq_tsv" />
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60 </when>
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61 <when value="entry">
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62 <param name="seq_text" type="text" label="Peptide Sequence"/>
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63 </when>
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64 </conditional>
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65 </xml>
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66 <xml name="citations">
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67 <citation type="doi">10.1093/nar/gku938</citation>
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68 <citation type="doi">10.1093/nar/gkaa379</citation>
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69 </xml>
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70 </macros>