Mercurial > repos > iuc > ncbi_eutils_esummary

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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 14:36:18 +0000
parents 254f40d3ae2b
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cb5a0fe9e036 "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_esummary" name="NCBI ESummary" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>fetch summary of history/ids</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 esummary.py --version</version_command>
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8 <command detect_errors="aggressive">
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9 <![CDATA[
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11 python '$__tool_directory__/esummary.py'
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13 $db_select
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15 @LIST_OR_HIST@
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17 @EMAIL_ARGUMENTS@
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19 #if $retstart is not None:
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20 --retstart '$retstart'
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21 #end if
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23 #if $retmax is not None:
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24 --retmax '$retmax'
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25 #end if
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27 #if $output_format == 'xml':
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28 --retmode xml
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29 #elif $output_format == 'json':
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30 --retmode json
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31 #end if
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33 > $default
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35 ]]>
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36 </command>
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37 <inputs>
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38 <expand macro="list_or_hist"/>
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39 <expand macro="dbselect"/>
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40 <param name="retstart" type="integer" value="0" min="0" max="99999" label="Starting record to return (--retstart)" />
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41 <param name="retmax" type="integer" value="100000" min="1" max="100000" label="Maximum number of records to return (--retmax)" />
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42 <param name="output_format" type="select" label="Output Format">
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43 <option value="xml" selected="True">XML</option>
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44 <option value="json">JSON</option>
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <data format="xml" name="default" label="Summary of NCBI Search">
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49 <change_format>
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50 <when input="output_format" value="xml" format="xml" />
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51 <when input="output_format" value="json" format="json" />
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52 </change_format>
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53 <filter>query_source['qss'] != 'history_json' and query_source['qss'] != 'history_xml'</filter>
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54 </data>
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55 <collection name="summaries" type="list" label="Summary of NCBI Searches">
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56 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
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57 <filter>query_source['qss'] == 'history_json' or query_source['qss'] == 'history_xml'</filter>
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58 </collection>
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59 </outputs>
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60 <tests>
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61 <test expect_num_outputs="1">
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62 <param name="qss" value="id_list"/>
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63 <param name="id_list" value="10239"/>
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64 <param name="db_select" value="taxonomy"/>
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65 <param name="retstart" value="0"/>
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66 <param name="retmax" value="100000"/>
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67 <param name="output_format" value="xml"/>
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68 <output name="default" file="esummary.tax.xml" ftype="xml"/>
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69 </test>
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70 </tests>
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71 <help><![CDATA[
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72 NCBI Entrez ESummary
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73 ====================
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75 Responds to a list of UIDs from a given database with the corresponding
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76 document summaries.
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78 Example Queries
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79 ---------------
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81 Search against protein:
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83 +----------------------+--------------------------------------+
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84 | Parameter | Value |
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85 +======================+======================================+
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86 | NCBI Database to Use | Protein |
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87 +----------------------+--------------------------------------+
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88 | ID List | 28800982 28628843 |
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89 +----------------------+--------------------------------------+
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90
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91 @REFERENCES@
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92
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93 @DISCLAIMER@
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94 ]]></help>
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95 <expand macro="citations"/>
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96 </tool>