Mercurial > repos > iuc > ncbi_eutils_efetch

annotate efetch.xml @ 9:6c4b39080ed7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 41f5eb8e0aee5b779d618b5178098c4be89a9ef1
author iuc
date Mon, 23 Jan 2023 10:37:57 +0000
parents 4194e47b45d4
children 0ccb2855dd55
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1 <?xml version="1.0"?>
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2 <tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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3 <description>fetch records from NCBI</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <version_command>python efetch.py --version</version_command>
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9 <command detect_errors="aggressive"><![CDATA[
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11 python '$__tool_directory__/efetch.py'
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13 $db.db_select
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15 @LIST_OR_HIST@
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17 @EMAIL_ARGUMENTS@
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19 @EFETCH_FORMAT_TOKEN@
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21 ]]></command>
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22 <inputs>
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23 <expand macro="list_or_hist"/>
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24 <expand macro="efetchdb"/>
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25 </inputs>
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26 <outputs>
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27 <collection name="output1" type="list" label="NCBI EFetch results">
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28 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
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29 </collection>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="db_select" value="taxonomy"/>
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34 <param name="output_format" value="none-xml-xml"/>
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35 <param name="qss" value="id_list"/>
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36 <param name="id_list" value="10239"/>
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37 <output_collection name="output1" type="list" count="1">
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38 <element name="EFetch-None-xml-chunk1" ftype="xml" file="viruses.tax.xml" lines_diff="2" />
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39 </output_collection>
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40 </test>
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41 <test>
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42 <param name="db_select" value="nuccore"/>
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43 <param name="output_format" value="fasta-text-fasta"/>
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44 <param name="qss" value="id_file"/>
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45 <param name="id_file" value="efetchin.tabular"/>
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46 <output_collection name="output1" type="list" count="1">
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47 <element name="EFetch-fasta-text-chunk1" ftype="fasta">
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48 <assert_contents>
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49 <has_text text="XM_036034467"/>
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50 <has_text text="NC_040910"/>
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51 </assert_contents>
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52 </element>
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53 </output_collection>
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54 </test>
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55 </tests>
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56 <help><![CDATA[
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57 NCBI Entrez EFetch
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58 ==================
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60 Responds to a list of UIDs in a given database with the corresponding data
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61 records in a specified format.
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63 Example Queries
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64 ---------------
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66 Fetch PMIDs 17284678 and 9997 as text abstracts:
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68 +----------------------+--------------------------------------+
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69 | Parameter | Value |
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70 +======================+======================================+
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71 | NCBI Database to Use | PubMed |
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72 +----------------------+--------------------------------------+
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73 | ID List | 17284678 9997 |
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74 +----------------------+--------------------------------------+
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75 | Output Format | Abstract |
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76 +----------------------+--------------------------------------+
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78 Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
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79
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80 +----------------------+--------------------------------------+
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81 | Parameter | Value |
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82 +======================+======================================+
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83 | NCBI Database to Use | Protein |
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84 +----------------------+--------------------------------------+
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85 | ID List | 312836839 34577063 |
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86 +----------------------+--------------------------------------+
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87 | Output Format | Fasta |
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88 +----------------------+--------------------------------------+
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89
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90 @REFERENCES@
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91
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92 @DISCLAIMER@
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93 ]]></help>
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94 <expand macro="citations"/>
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95 </tool>