Mercurial > repos > iuc > beacon2_gene
annotate gene.xml @ 2:477efaeac704 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 19:24:57 +0000 |
| parents | 7cde0f1d7d55 |
| children |
| rev | line source |
|---|---|
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0
9f64a2f52667
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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1 <tool id="beacon2_gene" name="Beacon2 Gene" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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9f64a2f52667
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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2 <description>Queries the beacon database and retrieve the genomic variants matching gene symbol</description> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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3 <macros> |
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9f64a2f52667
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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4 <import>macros.xml</import> |
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9f64a2f52667
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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5 </macros> |
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9f64a2f52667
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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6 <expand macro="creators"/> |
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9f64a2f52667
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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7 <expand macro="requirements"/> |
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9f64a2f52667
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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8 <command detect_errors="exit_code"><![CDATA[ |
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9f64a2f52667
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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9 beacon2-search gene |
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9f64a2f52667
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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10 --db-host '$db_host' |
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9f64a2f52667
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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11 --db-port $db_port |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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12 --database '$database' |
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9f64a2f52667
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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13 --collection '$collection' |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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14 --advance-connection |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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15 --db-auth-config '$credentials' |
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9f64a2f52667
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 --geneId $geneId |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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17 #if str($advanced_settings.alternateBases) |
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9f64a2f52667
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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18 --alternateBases '$advanced_settings.alternateBases' |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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19 #end if |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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20 #if str($advanced_settings.variantType) |
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9f64a2f52667
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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21 --variantType '$advanced_settings.variantType' |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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22 #end if |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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23 #if str($advanced_settings.aminoacidChange) |
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9f64a2f52667
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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24 --aminoacidChange '$advanced_settings.aminoacidChange' |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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25 #end if |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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26 #if str($advanced_settings.variantMinLength) |
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9f64a2f52667
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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27 --variantMinLength $advanced_settings.variantMinLength |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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28 #end if |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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29 #if str($advanced_settings.variantMaxLength) |
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9f64a2f52667
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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30 --variantMaxLength $advanced_settings.variantMaxLength |
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9f64a2f52667
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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31 #end if |
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9f64a2f52667
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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32 > gene_query_findings.json |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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33 ]]></command> |
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9f64a2f52667
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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34 <expand macro="configfile"/> |
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9f64a2f52667
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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35 <inputs> |
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9f64a2f52667
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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36 <expand macro="Connection_to_MongoDB" /> |
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9f64a2f52667
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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37 <expand macro="Database_Configuration" /> |
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9f64a2f52667
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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38 <param argument="--geneId" type="text" label="Gene Id" value="" help="" /> |
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9f64a2f52667
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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39 <section name="advanced_settings" title="Advanced settings" expanded="false"> |
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9f64a2f52667
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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40 <param argument="--alternateBases" optional="true" type="text" label="ALTERNATEBASES" value="" help="Targeted Alternate bases to search for" /> |
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9f64a2f52667
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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41 <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" /> |
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9f64a2f52667
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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42 <param argument="--aminoacidChange" optional="true" type="text" label="AMINOACID CHANGE" value="" help="Targeted Amino acid change to search for" /> |
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9f64a2f52667
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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43 <param argument="--variantMinLength" optional="true" type="integer" label="VARIANT MIN LENGTH" value="" help="Targeted Variant minimum length to search for" /> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
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44 <param argument="--variantMaxLength" optional="true" type="integer" label="VARIANT MAX LENGTH" value="" help="Targeted VVariant maximum length to search for" /> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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45 </section> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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46 </inputs> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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47 <outputs> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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48 <data name="out_gene_query" format="json" label="${tool.name} on ${on_string}: Gene Query" from_work_dir="gene_query_findings.json" /> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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49 </outputs> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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50 <tests> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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51 <test expect_num_outputs="1"> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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52 <param name="database" value="beacon" /> |
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1
7cde0f1d7d55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
iuc
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53 <param name="collection" value="test" /> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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54 <param name="db_host" value="20.108.51.167" /> |
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1
7cde0f1d7d55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
iuc
parents:
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55 <param name="geneId" value="BRCA1" /> |
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7cde0f1d7d55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
iuc
parents:
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56 <param name="variantType" value="SNV" /> |
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7cde0f1d7d55
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
iuc
parents:
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57 <param name="aminoacidChange" value="p.Val600Glu" /> |
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0
9f64a2f52667
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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58 <output name="out_gene_query"> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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59 <assert_contents><has_text_matching expression="_id"/></assert_contents> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
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60 </output> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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61 </test> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
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62 </tests> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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63 <help><![CDATA[ |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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64 GeneId Queries are in essence a variation of Range Queries in which the coordinates are replaced by the HGNC gene symbol. It is left to the implementation if the matching is done on variants annotated for the gene symbol or if a positional translation is being applied. |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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65 ]]></help> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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66 <expand macro="citations" /> |
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9f64a2f52667
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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67 </tool> |