Mercurial > repos > iuc > beacon2_datasets

annotate datasets.xml @ 1:237beddb2ab0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit 23f6d9e5e91c43d5ab68e604205e06785635f42f
author iuc
date Mon, 19 Aug 2024 10:49:53 +0000
parents 869126027692
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869126027692 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_datasets" name="Beacon2 Datasets" version="1.0.0" profile="21.05">
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2 <description>Query the datasets collection in the beacon database groupings of variants or individuals who belong to the same repository</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 datasets
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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($advanced_settings.dataUseConditions)
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18 --dataUseConditions '$advanced_settings.dataUseConditions'
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19 #end if
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20 #if str($advanced_settings.ontologyModifiers)
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21 --ontologyModifiers '$advanced_settings.ontologyModifiers'
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22 #end if
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23 #if str($advanced_settings.identification)
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24 --identification '$advanced_settings.identification'
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25 #end if
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26 #if str($advanced_settings.name)
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27 --name '$advanced_settings.name'
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28 #end if
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29 > datasets_query_findings.json
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30 ]]>
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31 </command>
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32 <expand macro="configfile"/>
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33 <inputs>
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34 <expand macro="Connection_to_MongoDB"/>
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35 <expand macro="Database_Configuration"/>
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36 <section name="advanced_settings" title="Advanced settings" expanded="false">
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37 <param argument="--dataUseConditions" optional="true" type="text" label="DATAUSECONDITIONS" value="" help="Data use conditions applying to this dataset, e.g. disease specific research" />
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38 <param argument="--ontologyModifiers" optional="true" type="text" label="DATA USE CONDITIONS MODIFIERS" value="" help="Modifiers that further specify the datasets, e.g. coronary artery disease" />
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39 <param argument="--identification" optional="true" type="text" label="ID" value="" help="Unique identifier of the dataset" />
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40 <param argument="--name" optional="true" type="text" label="NAME" value="" help="Name of the dataset" />
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41 </section>
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42 </inputs>
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43 <outputs>
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44 <data name="out_datasets_query" format="json" label="${tool.name} on ${on_string}: Datasets Query" from_work_dir="datasets_query_findings.json" />
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45 </outputs>
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46 <tests>
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47 <test expect_num_outputs="1">
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48 <param name="database" value="beacon" />
1
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49 <param name="collection" value="test" />
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50 <param name="db_host" value="20.108.51.167" />
1
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51 <param name="identification" value="refvar-66bf2f5ead2a4a766ce987ee" />
0
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52 <param name="name" value="The Genome in a Bottle Consortium (GIAB)" />
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53 <output name="out_datasets_query">
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54 <assert_contents>
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55 <has_text_matching expression="_id"/>
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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60 <help><![CDATA[
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61 Beacon2 Datasets queries the datasets collection in the Beacon database to study the variants or individuals in a populations or groups who belong to the same repository.
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62 ]]></help>
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63 <expand macro="citations" />
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64 </tool>