Mercurial > repos > iuc > beacon2_bracket

annotate bracket.xml @ 0:2e60de9f5046 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
author iuc
date Mon, 22 Jul 2024 12:35:01 +0000
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children 3347fc9c43bf
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2e60de9f5046 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_bracket" name="Beacon2 Bracket" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Specifies a sequence ranges for both the start and end positions of a genomic variation</description>
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3 <macros>
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iuc
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4 <import>macros.xml</import>
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5 </macros>
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iuc
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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 bracket
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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-minimum $start_minimum
2e60de9f5046 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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17 --start-maximum $start_maximum
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18 --end-minimum $end_minimum
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19 --end-maximum $end_maximum
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20 #if str($advanced_settings.variantType)
2e60de9f5046 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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21 --variantType '$advanced_settings.variantType'
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22 #end if
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23 #if str($advanced_settings.referenceName)
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24 --referenceName '$advanced_settings.referenceName'
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25 #end if
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iuc
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26 > bracket_query_findings.json
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27 ]]></command>
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iuc
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28 <expand macro="configfile"/>
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29 <inputs>
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30 <expand macro="Connection_to_MongoDB" />
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31 <expand macro="Database_Configuration" />
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32 <param argument="--start-minimum" type="integer" label="Start minimum position" value="" help="" />
2e60de9f5046 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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33 <param argument="--start-maximum" type="integer" label="Start maximum position" value="" help="" />
2e60de9f5046 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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34 <param argument="--end-minimum" type="integer" label="End minimum position" value="" help="" />
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35 <param argument="--end-maximum" type="integer" label="End maximum position" value="" help="" />
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36 <section name="advanced_settings" title="Advanced settings" expanded="false">
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37 <param argument="--referenceName" optional="true" type="text" label="Reference Name" value="" help="Reference name in numbers chr1/1, chr2/2, chr3/3, etc." />
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38 <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Targeted Variant type to search for" />
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39 </section>
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40 </inputs>
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41 <outputs>
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42 <data name="out_bracket_query" format="json" label="${tool.name} on ${on_string}: Bracket Query" from_work_dir="bracket_query_findings.json" />
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43 </outputs>
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44 <tests>
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45 <test expect_num_outputs="1">
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46 <param name="database" value="beacon" />
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47 <param name="collection" value="genomicVariations" />
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48 <param name="db_host" value="20.108.51.167" />
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49 <param name="start_minimum" value="131836" />
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50 <param name="start_maximum" value="161836" />
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51 <param name="end_minimum" value="131837" />
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52 <param name="end_maximum" value="151837" />
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53 <param name="variantType" value="SNP" />
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54 <output name="out_bracket_query">
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55 <assert_contents><has_text_matching expression="_id"/></assert_contents>
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56 </output>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 Bracket Queries allow the specification of sequence ranges for both start and end positions of a genomic variation. The typical example here is the query for similar structural variants - particularly CNVs - affecting a genomic region but potentially differing in their exact base extents.
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61 ]]></help>
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62 <expand macro="citations" />
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63 </tool>