Mercurial > repos > iuc > beacon2_range

annotate range.xml @ 2:efc729d8540d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit bf308a3ea09dc413670e41141d6849af7dd33798
author iuc
date Tue, 24 Sep 2024 19:24:27 +0000
parents 6b2ef850f7af
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36cd015a8eea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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1 <tool id="beacon2_range" name="Beacon2 Range" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Retrieve the genomic variants from the beacon database by specifying start and end positions</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creators"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 beacon2-search range
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10 --db-host '$db_host'
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11 --db-port $db_port
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12 --database '$database'
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13 --collection '$collection'
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14 --advance-connection
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15 --db-auth-config '$credentials'
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16 --start $start
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17 --end $end
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18 #if str($advanced_settings.referenceName)
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19 --referenceName '$advanced_settings.referenceName'
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20 #end if
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21 #if str($advanced_settings.alternateBases)
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22 --alternateBases '$advanced_settings.alternateBases'
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23 #end if
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24 #if str($advanced_settings.variantType)
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25 --variantType '$advanced_settings.variantType'
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26 #end if
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27 #if str($advanced_settings.aminoacidChange)
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28 --aminoacidChange '$advanced_settings.aminoacidChange'
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29 #end if
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30 #if str($advanced_settings.variantMinLength)
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31 --variantMinLength $advanced_settings.variantMinLength
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32 #end if
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33 #if str($advanced_settings.variantMaxLength)
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34 --variantMaxLength $advanced_settings.variantMaxLength
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35 #end if
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36 > ranged_query_findings.json
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37 ]]></command>
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38 <expand macro="configfile"/>
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39 <inputs>
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40 <expand macro="Connection_to_MongoDB" />
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41 <expand macro="Database_Configuration" />
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42 <param argument="--start" type="integer" label="START" value="" help="Start position" />
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43 <param argument="--end" type="integer" label="END" value="" help="End position" />
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44 <section name="advanced_settings" title="Advanced settings" expanded="false">
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45 <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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46 <param argument="--alternateBases" optional="true" type="text" label="ALTERNATEBASES" value="" help="Targeted Alternate bases to search for" />
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47 <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
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48 <param argument="--aminoacidChange" optional="true" type="text" label="AMINOACID CHANGE" value="" help="Targeted Amino acid change to search for" />
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49 <param argument="--variantMinLength" optional="true" type="integer" label="VARIANT MIN LENGTH" value="" help="Targeted Variant minimum length to search for" />
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50 <param argument="--variantMaxLength" optional="true" type="integer" label="VARIANT MAX LENGTH" value="" help="Targeted VVariant maximum length to search for" />
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51 </section>
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52 </inputs>
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53 <outputs>
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54 <data name="out_ranged_query" format="json" label="${tool.name} on ${on_string}: Range Query" from_work_dir="ranged_query_findings.json" />
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55 </outputs>
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56 <tests>
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57 <test expect_num_outputs="1">
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58 <param name="database" value="beacon" />
1
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59 <param name="collection" value="test" />
0
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60 <param name="db_host" value="20.108.51.167" />
1
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61 <param name="start" value="12345" />
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62 <param name="end" value="67900" />
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63 <param name="variantType" value="SNV" />
0
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64 <output name="out_ranged_query">
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65 <assert_contents><has_text_matching expression="_id"/></assert_contents>
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66 </output>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 Beacon Range Queries are supposed to return matches of any variant with at least partial overlap of the sequence range specified by reference_name, start and end parameters
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71 ]]></help>
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72 <expand macro="citations" />
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73 </tool>