Mercurial > repos > iuc > beacon2_sequence
annotate sequence.xml @ 2:baa5e8287579 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit bf308a3ea09dc413670e41141d6849af7dd33798
| author | iuc |
|---|---|
| date | Tue, 24 Sep 2024 19:25:27 +0000 |
| parents | 94f3eb8da2b3 |
| children |
| rev | line source |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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1 <tool id="beacon2_sequence" name="Beacon2 Sequence" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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2 <description>ŁQuery for the existence of a specified sequence at a given genomic position</description> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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3 <macros> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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4 <import>macros.xml</import> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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5 </macros> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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6 <expand macro="creators"/> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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7 <expand macro="requirements"/> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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8 <command detect_errors="exit_code"><![CDATA[ |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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9 beacon2-search sequence |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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10 --db-host '$db_host' |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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11 --db-port $db_port |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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12 --database '$database' |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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13 --collection '$collection' |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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14 --advance-connection |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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15 --db-auth-config '$credentials' |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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16 --alternateBases '$alternateBases' |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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17 --referenceBases '$referenceBases' |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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18 #if str($advanced_settings.referenceName) |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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19 --referenceName '$advanced_settings.referenceName' |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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20 #end if |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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21 #if str($advanced_settings.start) |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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22 --start $advanced_settings.start |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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23 #end if |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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24 #if str($advanced_settings.collectionIds) |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
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25 --collectionIds '$advanced_settings.collectionIds' |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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26 #end if |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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changeset
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27 > sequenced_query_findings.json |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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28 ]]></command> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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29 <expand macro="configfile"/> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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30 <inputs> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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31 <expand macro="Connection_to_MongoDB" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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32 <expand macro="Database_Configuration" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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33 <param argument="--alternateBases" type="text" label="Alternate bases" value="" help="" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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34 <param argument="--referenceBases" type="text" label="Reference bases" value="" help="" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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35 <section name="advanced_settings" title="Advanced settings" expanded="false"> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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36 <param argument="--referenceName" optional="true" type="text" label="REFERENCENAME" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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37 <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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38 <param argument="--collectionIds" optional="true" type="text" label="Collection ID" value="" help="Datasets ID" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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39 </section> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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40 </inputs> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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41 <outputs> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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42 <data name="out_sequence_query" format="json" label="${tool.name} on ${on_string}: Sequence Query" from_work_dir="sequenced_query_findings.json" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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43 </outputs> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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44 <tests> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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45 <test expect_num_outputs="1"> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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46 <param name="database" value="beacon" /> |
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1
94f3eb8da2b3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
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47 <param name="collection" value="test" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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48 <param name="db_host" value="20.108.51.167" /> |
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1
94f3eb8da2b3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
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49 <param name="start" value="100000" /> |
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94f3eb8da2b3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
iuc
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50 <param name="alternateBases" value="G" /> |
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94f3eb8da2b3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
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51 <param name="referenceBases" value="T" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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52 <output name="out_sequence_query"> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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53 <assert_contents><has_text_matching expression="_id"/></assert_contents> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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54 </output> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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55 </test> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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56 </tests> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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57 <help><![CDATA[ |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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58 Sequence Queries query for the existence of a specified sequence at a given genomic position. Such queries correspond to the original Beacon queries and are used to match short, precisely defined genomic variants such as SNVs and INDELs. |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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59 ]]></help> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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60 <expand macro="citations" /> |
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f14c8c011f01
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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61 </tool> |