Mercurial > repos > iuc > beacon2_gene
annotate gene.xml @ 1:9135f3e914b7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
author | iuc |
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date | Mon, 19 Aug 2024 10:54:54 +0000 |
parents | 8e949a739eaa |
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rev | line source |
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0
8e949a739eaa
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_gene" name="Beacon2 Gene" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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2 <description>Queries the beacon database and retrieve the genomic variants matching gene symbol</description> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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3 <macros> |
8e949a739eaa
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> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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5 </macros> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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6 <expand macro="creators"/> |
8e949a739eaa
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"/> |
8e949a739eaa
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[ |
8e949a739eaa
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 gene |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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10 --db-host '$db_host' |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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11 --db-port $db_port |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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12 --database '$database' |
8e949a739eaa
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 '$collection' |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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14 --advance-connection |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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15 --db-auth-config '$credentials' |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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16 --geneId $geneId |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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17 #if str($advanced_settings.alternateBases) |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
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18 --alternateBases '$advanced_settings.alternateBases' |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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19 #end if |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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20 #if str($advanced_settings.variantType) |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
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21 --variantType '$advanced_settings.variantType' |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
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22 #end if |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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23 #if str($advanced_settings.aminoacidChange) |
8e949a739eaa
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 '$advanced_settings.aminoacidChange' |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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25 #end if |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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26 #if str($advanced_settings.variantMinLength) |
8e949a739eaa
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 $advanced_settings.variantMinLength |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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28 #end if |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
changeset
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29 #if str($advanced_settings.variantMaxLength) |
8e949a739eaa
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 |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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31 #end if |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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32 > gene_query_findings.json |
8e949a739eaa
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> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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34 <expand macro="configfile"/> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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35 <inputs> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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36 <expand macro="Connection_to_MongoDB" /> |
8e949a739eaa
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" /> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
diff
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38 <param argument="--geneId" type="text" label="Gene Id" value="" help="" /> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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39 <section name="advanced_settings" title="Advanced settings" expanded="false"> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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40 <param argument="--alternateBases" optional="true" type="text" label="ALTERNATEBASES" value="" help="Targeted Alternate bases to search for" /> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
parents:
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41 <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" /> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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42 <param argument="--aminoacidChange" optional="true" type="text" label="AMINOACID CHANGE" value="" help="Targeted Amino acid change to search for" /> |
8e949a739eaa
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" /> |
8e949a739eaa
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" /> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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45 </section> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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46 </inputs> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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47 <outputs> |
8e949a739eaa
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" /> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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49 </outputs> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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50 <tests> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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51 <test expect_num_outputs="1"> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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52 <param name="database" value="beacon" /> |
1
9135f3e914b7
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" /> |
0
8e949a739eaa
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" /> |
1
9135f3e914b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
iuc
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55 <param name="geneId" value="BRCA1" /> |
9135f3e914b7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
iuc
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56 <param name="variantType" value="SNV" /> |
9135f3e914b7
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" /> |
0
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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58 <output name="out_gene_query"> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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59 <assert_contents><has_text_matching expression="_id"/></assert_contents> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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60 </output> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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61 </test> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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62 </tests> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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63 <help><![CDATA[ |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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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. |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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65 ]]></help> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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66 <expand macro="citations" /> |
8e949a739eaa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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67 </tool> |