Mercurial > repos > iuc > beacon2_cnv

annotate cnv.xml @ 3:ccb79738093c 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 19:25:20 +0000
parents be168523dcf7
children
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2dd335ce7dba 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_cnv" name="Beacon2 CNV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Retrieve the copy number varients from genomicVariations collection from the beacon database</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 cnv
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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 #if str($advanced_settings.variantInternalId)
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17 --variantInternalId '$advanced_settings.variantInternalId'
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18 #end if
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19 #if str($advanced_settings.analysisId)
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20 --analysisId '$advanced_settings.analysisId'
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21 #end if
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22 #if str($advanced_settings.individualId)
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23 --individualId '$advanced_settings.individualId'
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24 #end if
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25 #if str($advanced_settings.start)
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26 --start $advanced_settings.start
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27 #end if
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28 #if str($advanced_settings.end)
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29 --end $advanced_settings.end
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30 #end if
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31 #if str($advanced_settings.chromosome)
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32 --chromosome '$advanced_settings.chromosome'
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33 #end if
1
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34 #if str($advanced_settings.variantStateId) and $advanced_settings.variantStateId != ""
0
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35 --variantStateId '$advanced_settings.variantStateId'
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36 #end if
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37 #if str($advanced_settings.sequenceId)
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38 --sequenceId '$advanced_settings.sequenceId'
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39 #end if
1
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40 #if str($advanced_settings.variantType)
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41 --variantType '$advanced_settings.variantType'
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42 #end if
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43 #if str($advanced_settings.primarySite)
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44 --primarySite '$advanced_settings.primarySite'
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45 #end if
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46 #if str($advanced_settings.diseaseType)
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47 --diseaseType '$advanced_settings.diseaseType'
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48 #end if
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49 #if str($advanced_settings.gene)
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50 --gene '$advanced_settings.gene'
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51 #end if
0
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52 > cnv_query_findings.json
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53 ]]></command>
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54 <expand macro="configfile"/>
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55 <inputs>
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56 <expand macro="Connection_to_MongoDB" />
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57 <expand macro="Database_Configuration" />
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58 <section name="advanced_settings" title="Advanced settings" expanded="false">
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59 <param argument="--variantInternalId" optional="true" type="text" label="VARIANT INTERNAL ID" value="" help="E.g. 11:52900000-134452384:DEL" />
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60 <param argument="--analysisId" optional="true" type="text" label="ANALYSIS ID" value="" help="" />
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61 <param argument="--individualId" optional="true" type="text" label="INDIVIDUAL ID" value="" help="" />
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62 <param argument="--start" optional="true" type="integer" label="START" value="" help="Start position" />
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63 <param argument="--end" optional="true" type="integer" label="END" value="" help="End position" />
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64 <param argument="--chromosome" optional="true" type="text" label="CHROMOSOME" value="" help="Chromosome numbers (without chr)" />
2
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65 <param argument="variantStateId" optional="true" type="select" label="VARIANT STATE" help="">
1
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66 <option value="EFO:0030070">EFO:0030070: copy number gain</option>
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67 <option value="EFO:0030071">EFO:0030071: low-level copy number gain</option>
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68 <option value="EFO:0030072">EFO:0030072: high-level copy number gain</option>
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69 <option value="EFO:0030073">EFO:0030073: focal genome amplification</option>
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70 <option value="EFO:0030067">EFO:0030067: copy number loss</option>
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71 <option value="EFO:0030068">EFO:0030068: low-level copy number loss</option>
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72 <option value="EFO:0020073">EFO:0020073: high-level copy number loss</option>
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73 <option value="EFO:0030069">EFO:0030069: complete genomic deletion</option>
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74 <option value="" selected="True">non specific</option>
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75 </param>
0
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76 <param argument="--sequenceId" optional="true" type="text" label="SEQUENCE ID" value="" help="E.g. refseq:NC_000011.10" />
1
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77 <param argument="--gene" optional="true" type="text" label="GENE NAME" value="" help="Gene name e.g. 'AL645728.1'" />
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78 <param argument="--variantType" optional="true" type="text" label="VARIANT TYPE" value="" help="Variant Type 'DEL' or 'DUP'" />
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79 <param argument="--primarySite" optional="true" type="text" label="PRIMARY SITE" value="" help="Primary Site, e.g. 'brain'" />
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80 <param argument="--diseaseType" optional="true" type="text" label="DISEASE TYPE" value="" help="Disease Type, e.g. 'adnexal and skin appendage neoplasms'" />
0
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81 </section>
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82 </inputs>
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83 <outputs>
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84 <data name="out_cnv_query" format="json" label="${tool.name} on ${on_string}: CNV Query" from_work_dir="cnv_query_findings.json" />
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85 </outputs>
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86 <tests>
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87 <test expect_num_outputs="1">
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88 <param name="database" value="beacon" />
1
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89 <param name="collection" value="test" />
0
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90 <param name="db_host" value="20.108.51.167" />
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91 <param name="chromosome" value="17" />
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92 <param name="start" value="43044295" />
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93 <param name="end" value="43170245" />
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94 <param name="primarySite" value="breast" />
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95 <param name="diseaseType" value="adnexal and skin appendage neoplasms" />
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96 <param name="gene" value="BRCA1" />
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97 <param name="variantStateId" value="EFO:0030068" />
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98 <output name="out_cnv_query">
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99 <assert_contents><has_text_matching expression="_id"/></assert_contents>
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100 </output>
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101 </test>
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102 </tests>
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103 <help><![CDATA[
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104 Beacon CNV Queries are supposed to return matches of any copy number variants with at least partial overlap of the input parameters
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105 ]]></help>
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106 <expand macro="citations" />
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107 </tool>