Mercurial > repos > iuc > beacon2_individuals

annotate individuals.xml @ 2:5afecf44cdb5 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 19:23:49 +0000
parents 48ef001d5f05
children
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49c9a2fb548b 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_individuals" name="Beacon2 Individuals" version="1.0.0" profile="21.05">
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2 <description>Query the individuals collection in 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">
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9 <![CDATA[
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10 beacon2-search individuals
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11 --db-host '$db_host'
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12 --db-port $db_port
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13 --database '$database'
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14 --collection '$collection'
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15 --advance-connection
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16 --db-auth-config '$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'
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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($advanced_settings.severity)
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27 --severity '$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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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($advanced_settings.geographicOrigin)
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36 --geographicOrigin '$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" />
1
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81 <param name="collection" value="test" />
0
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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"/>
49c9a2fb548b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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90 </assert_contents>
49c9a2fb548b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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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[
49c9a2fb548b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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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.
49c9a2fb548b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
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96 ]]></help>
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97 <expand macro="citations" />
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98 </tool>