Mercurial > repos > iuc > beacon2_individuals

annotate individuals.xml @ 0:b648eb72552c 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 12:35:16 +0000
parents
children 72d8cb0fa73f
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0
b648eb72552c 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_individuals" name="Beacon2 Individuals" version="1.0.0" profile="21.05">
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iuc
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2 <description>Query the individuals collection in the beacon database</description>
b648eb72552c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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3 <macros>
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iuc
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4 <import>macros.xml</import>
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iuc
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5 </macros>
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iuc
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6 <expand macro="creators"/>
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iuc
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7 <expand macro="requirements"/>
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iuc
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8 <command detect_errors="exit_code">
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9 <![CDATA[
b648eb72552c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
iuc
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10 beacon2-search individuals
b648eb72552c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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11 --db-host '$db_host'
b648eb72552c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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12 --db-port $db_port
b648eb72552c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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13 --database '$database'
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iuc
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14 --collection '$collection'
b648eb72552c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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15 --advance-connection
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16 --db-auth-config '$credentials'
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17 #if str($advanced_settings.ageGroup)
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18 --ageGroup '$advanced_settings.ageGroup'
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19 #end if
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20 #if str($advanced_settings.diseaseCode)
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21 --diseaseCode '$advanced_settings.diseaseCode'
b648eb72552c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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22 #end if
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23 #if str($advanced_settings.familyHistory) and $advanced_settings.familyHistory != ""
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24 --familyHistory '$advanced_settings.familyHistory'
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25 #end if
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26 #if str($advanced_settings.severity)
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iuc
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27 --severity '$advanced_settings.severity'
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28 #end if
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29 #if str($advanced_settings.stage)
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30 --stage '$advanced_settings.stage'
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31 #end if
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iuc
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32 #if str($advanced_settings.ethnicity)
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33 --ethnicity '$advanced_settings.ethnicity'
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34 #end if
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35 #if str($advanced_settings.geographicOrigin)
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iuc
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36 --geographicOrigin '$advanced_settings.geographicOrigin'
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37 #end if
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38 #if str($advanced_settings.identification)
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39 --identification '$advanced_settings.identification'
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40 #end if
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41 #if str($advanced_settings.assayCode)
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42 --assayCode '$advanced_settings.assayCode'
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43 #end if
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44 #if str($advanced_settings.sex) and $advanced_settings.sex != ""
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45 --sex '$advanced_settings.sex'
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46 #end if
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47 > individuals_query_findings.json
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48 ]]>
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49 </command>
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50 <expand macro="configfile"/>
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51 <inputs>
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52 <expand macro="Connection_to_MongoDB"/>
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53 <expand macro="Database_Configuration"/>
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54 <section name="advanced_settings" title="Advanced settings" expanded="false">
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55 <param argument="--ageGroup" optional="true" type="text" label="AGE GROUP" value="" help="age af onset, e.g. Adult 18-65 Years Old" />
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56 <param argument="--diseaseCode" optional="true" type="text" label="DISEASE CODE" value="" help="Disease code, Spinocerebellar ataxia 1" />
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57 <param argument="--familyHistory" optional="true" type="select" label="FAMILY HISTORY" help="">
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58 <option value="true">true</option>
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59 <option value="false">false</option>
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60 <option value="" selected="True">unknown</option>
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61 </param>
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62 <param argument="--severity" optional="true" type="text" label="SEVERITY" value="" help="e.g. Profound" />
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63 <param argument="--stage" optional="true" type="text" label="STAGE" value="" help="e.g. acute onset" />
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64 <param argument="--ethnicity" optional="true" type="text" label="ETHNICITY" value="" help="e.g. European" />
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65 <param argument="--geographicOrigin" optional="true" type="text" label="GEOGRAPHIC ORIGIN" value="" help="e.g. Slovenia" />
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66 <param argument="--identification" optional="true" type="text" label="ID" value="" help="Individual identifier (internal ID)" />
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67 <param argument="--assayCode" optional="true" type="text" label="ASSAY CODE" value="" help="e.g. Platelets [#/volume] in Blood" />
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68 <param argument="--sex" optional="true" type="select" label="SEX" help="">
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69 <option value="male">male</option>
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70 <option value="female">female</option>
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71 <option value="" selected="True">non specific</option>
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72 </param>
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73 </section>
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74 </inputs>
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75 <outputs>
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76 <data name="out_individuals_query" format="json" label="${tool.name} on ${on_string}: Individuals Query" from_work_dir="individuals_query_findings.json" />
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77 </outputs>
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78 <tests>
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79 <test expect_num_outputs="1">
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80 <param name="database" value="beacon" />
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81 <param name="collection" value="individuals" />
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82 <param name="db_host" value="20.108.51.167" />
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83 <param name="sex" value="male" />
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84 <param name="geographicOrigin" value="United States of America" />
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85 <param name="diseaseCode" value="intolerance" />
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86 <param name="ethnicity" value="Han Chinese" />
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87 <output name="out_individuals_query">
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88 <assert_contents>
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89 <has_text_matching expression="_id"/>
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90 </assert_contents>
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91 </output>
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92 </test>
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93 </tests>
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94 <help><![CDATA[
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95 Beacon2 Individuals queries the individuals collection in the Beacon database for either patients or healthy controls whose details (including phenotypic and clinical) are stored in the repository.
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96 ]]></help>
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97 <expand macro="citations" />
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98 </tool>