Mercurial > repos > iuc > ncbi_eutils_einfo

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 851b88d92fa7740880a5edf407f629bf3f7f7bf0
author iuc
date Fri, 04 Oct 2024 14:34:53 +0000
parents 62b0fc1d9184
children
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6d4fb70303b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
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1 <tool id="ncbi_eutils_einfo" name="NCBI EInfo" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>fetch NCBI database metadata</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="requirements"/>
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7 <version_command>python einfo.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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10 python '$__tool_directory__/einfo.py'
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12 #if $query_type.query_type == 'Description':
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13 --db $query_type.db_select
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14 #end if
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16 @EMAIL_ARGUMENTS@
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18 > $default
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19
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20 ]]></command>
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21 <inputs>
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22 <conditional name="query_type">
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23 <param name="query_type" type="select" label="Database Information Request Type" help="List databases or describe a database.">
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24 <option value="list" selected="True">List available databases</option>
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25 <option value="Description">Describe a database</option>
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26 </param>
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27 <when value="list">
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28 <param name="db_select" type="hidden" value="Database List"/>
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29 </when>
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30 <when value="Description">
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31 <expand macro="dbselect"/>
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32 </when>
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33 </conditional>
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34 </inputs>
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35 <outputs>
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36 <data format="xml" name="default" label="NCBI Database Information: $query_type.db_select"/>
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="query_type" value="Description"/>
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41 <param name="db_select" value="pubmed"/>
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42 <output name="default" file="pubmed.metadata.xml" compare="re_match_multiline" ftype="xml">
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43 <assert_contents>
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44 <is_valid_xml/>
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45 </assert_contents>
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46 </output>
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47 </test>
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48 <test>
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49 <param name="query_type" value="list"/>
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50 <param name="db_select" value="Database list"/>
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51 <output name="default" ftype="xml">
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52 <assert_contents>
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53 <has_text text="&lt;DbName&gt;pubmed&lt;/DbName&gt;"/>
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54 <is_valid_xml/>
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55 </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 NCBI Entrez EInfo
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61 =================
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63 Provides the number of records indexed in each field of a given database, the
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64 date of the last update of the database, and the available links from the
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65 database to other Entrez databases.
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67 @REFERENCES@
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69 @DISCLAIMER@
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70 ]]></help>
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71 <expand macro="citations"/>
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72 </tool>