Mercurial > repos > erasmus-medical-center > hla_dq

annotate hla_dq.xml @ 0:10a407fb5072 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
author erasmus-medical-center
date Wed, 30 May 2018 07:50:21 -0400
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children 4fc47a3ff9e8
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0
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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1 <tool id="hla_dq" name="HLA-DQ typing" version="1.0">
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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2 <description> Determine possible associated types given BLAST IMGT/HLA annotation</description>
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3 <command detect_errors="exit_code"><![CDATA[
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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4 python '$__tool_directory__/hla_dq.py'
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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5 #for $i in $filesA:
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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6 -A '$i.A'
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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7 #end for
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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8 #for $i in $filesB:
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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9 -B '$i.B'
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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10 #end for
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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11 #if $column and $column is not None:
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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12 --column $column
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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13 #end if
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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14 ]]></command>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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15 <inputs>
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16 <!-- use repeats cuz order matters -->
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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17 <repeat name="filesA" title="BLAST results A gene sequences" min="1">
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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18 <param argument="-A" label="BLAST IMGT/HLA hits A gene" type="data" format="tabular"/>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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19 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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20 <repeat name="filesB" title="BLAST results B gene sequences" min="1">
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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21 <param argument="-B" label="BLAST IMGT/HLA hits B gene" type="data" format="tabular"/>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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22 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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23 <param argument="--column" label="Column number containing the BLAST IMGT/HLA genotype annotation" type="integer" value="5" min="1" help="Example annotation: HLA:HLA11066 DQA1*01:05:02 768 bp"/>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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24 </inputs>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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25 <outputs>
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26 <data name="serotype_table" format="tabular" from_work_dir="results.tsv" label="${tool.name} on ${on_string}: Serotype table"/>
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27 </outputs>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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28 <tests>
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29 <test><!-- test with real data -->
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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30 <repeat name="filesA">
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31 <param name="A" value="sideA1.blast.tsv"/>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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32 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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33 <repeat name="filesA">
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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34 <param name="A" value="sideA2.blast.tsv"/>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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35 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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36 <repeat name="filesB">
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37 <param name="B" value="sideB1.blast.tsv"/>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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38 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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39 <repeat name="filesB">
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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40 <param name="B" value="sideB2.blast.tsv"/>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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41 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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42 <output name="serotype_table" file="test1_results.tsv"/>
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43 </test>
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44 <test><!-- test three files each and data leading to serotypes -->
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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45 <repeat name="filesA">
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46 <param name="A" value="sideA1.blast.tsv"/>
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47 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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48 <repeat name="filesA">
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49 <param name="A" value="sideA2.blast.tsv"/>
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50 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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51 <repeat name="filesA">
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52 <param name="A" value="all_sideA3.blast.tsv"/>
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53 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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54 <repeat name="filesB">
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55 <param name="B" value="sideB1.blast.tsv"/>
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56 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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57 <repeat name="filesB">
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58 <param name="B" value="sideB2.blast.tsv"/>
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59 </repeat>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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60 <repeat name="filesB">
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61 <param name="B" value="all_sideB3.blast.tsv"/>
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62 </repeat>
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63 <output name="serotype_table" file="test2_results.tsv"/>
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64 </test>
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65 </tests>
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66
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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67 <help><![CDATA[
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68
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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69 Given files annotated with BLAST and IMGT/HLA database for HLA-A and HLA-B gene (one or more files each), determine possible associated serotypes.
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70
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71 ===== ===== =====
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72 DQA1 DQB1 type
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73 ===== ===== =====
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74 02:01 02:02 DQ2.2
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75 03:03 02:02 DQ2.3
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76 05:01 02:01 DQ2.3
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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77 03:01 03:02 DQ8
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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78 03:02 03:02 DQ8
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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79 03:03 03:02 DQ8
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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80 ===== ===== =====
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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81
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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82 Example result table:
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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83
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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84 ==== ==== =========
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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85 type A1 A2
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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86 ==== ==== =========
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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87 B1 DQ8 None
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
erasmus-medical-center
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88 B2 None DQ2.2;DQ8
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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89 ==== ==== =========
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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90
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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91 Where A1, A2 correspond to two annotated input files given for gene A, each representing possible allele sequence
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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92
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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93 ]]></help>
10a407fb5072 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/hla_dq commit d6273a8247a1cbb7df2b26b9e97cd1bd3faa4f61
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94 </tool>