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0
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1 <tool id="pvac-seq" name="PVAC-seq" version="0.1.0">
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2
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2 <environment_variables>
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3 <environment_variable name="IEDB_INSTALL_DIRECTORY">$IEDB_INSTALL_DIRECTORY</environment_variable>
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4 </environment_variables>
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0
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5 <command detect_errors="exit_code"><![CDATA[
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6 #if str( $epitope_length ) != "":
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7 #set $epitope_length = "-e " + str($epitope_length)
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8 #end if
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9 #set algs = ' '.join([str($alg) for $alg in $algorithms])
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10 pvacseq run
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11 ${epitope_length}
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1
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12 --iedb-install-directory $IEDB_INSTALL_DIRECTORY
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0
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13 --tdna-vaf ${tdna_vaf}
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14 --net-chop-method ${net_chop_method}
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15 ${net_mhc_stab}
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16 --top-score-metric ${top_score_metric}
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17 --downstream-sequence-length ${downstream_sequence_length}
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18 ${input_vcf}
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19 galaxy
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20 ${allele}
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21 ${algs}
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22 `pwd` && mv MHC_Class_II/galaxy.final.tsv $output
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23
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24 ]]></command>
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25 <inputs>
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26 <param type="data" name="input_vcf" format="vcf" />
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27 <param type="text" name="allele" />
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28 <param name="algorithms" type="select" multiple="true" label="Epitope prediction algorithms">
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29 <option value="NNalign">NNalign</option>
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30 <option value="NetMHC">NetMHC</option>
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31 <option value="NetMHCIIpan">NetMHCIIpan</option>
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32 <option value="NetMHCcons">NetMHCcons</option>
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33 <option value="NetMHCpan">NetMHCpan</option>
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34 <option value="PickPocket">PickPocket</option>
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35 <option value="SMMPMBEC">SMMPMBEC</option>
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36 <option value="SMMalign">SMMalign</option>
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37 </param>
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38
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39 <param type="text" name="epitope_length"/>
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40 <param type="text" name="downstream_sequence_length" value="1000" help="int or 'full'"/>
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41 <param type="text" name="tdna_vaf" value="40"/>
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42 <param name="net_chop_method" type="select" label="NetChop prediction method">
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43 <option value="cterm">cterm</option>
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44 <option value="20s">20S</option>
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45 </param>
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46 <param name="net_mhc_stab" type="select" label="Run NetMHCStabPan after all filtering?">
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47 <option value="--netmhc-stab">Yes</option>
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48 <option value="">No</option>
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49 </param>
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50 <param name="top_score_metric" type="select" label="The ic50 scoring metric to use">
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51 <option value="median">Median</option>
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52 <option value="lowest">Lowest</option>
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53 </param>
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54 </inputs>
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55 <outputs>
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56 <data name="output" format="tabular"/>
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57 </outputs>
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58 <help><![CDATA[
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59 TODO: Fill in help.
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60 ]]></help>
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61 </tool> |
