Mercurial > repos > iuc > ncbi_eutils_efetch

annotate efetch.xml @ 15:cb4d6f20aacc draft default tip

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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 14:33:32 +0000
parents 172a4c4f4844
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1 <tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>fetch records from NCBI</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 efetch.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9
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10 python '$__tool_directory__/efetch.py'
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12 $db.db_select
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14 @LIST_OR_HIST@
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16 @EMAIL_ARGUMENTS@
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18 @EFETCH_FORMAT_TOKEN@
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20 ]]></command>
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21 <inputs>
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22 <expand macro="list_or_hist"/>
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23 <expand macro="efetchdb"/>
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24 </inputs>
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25 <outputs>
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26 <collection name="output1" type="list" label="NCBI EFetch results">
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27 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
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28 </collection>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="db_select" value="taxonomy"/>
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33 <param name="output_format" value="none-xml-xml"/>
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34 <param name="qss" value="id_list"/>
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35 <param name="id_list" value="10239"/>
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36 <output_collection name="output1" type="list" count="1">
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37 <element name="EFetch-None-xml-chunk1" ftype="xml" file="viruses.tax.xml" lines_diff="2" />
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38 </output_collection>
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39 </test>
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40 <test>
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41 <param name="db_select" value="nuccore"/>
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42 <param name="output_format" value="fasta-text-fasta"/>
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43 <param name="qss" value="id_file"/>
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44 <param name="id_file" value="efetchin.tabular"/>
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45 <output_collection name="output1" type="list" count="1">
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46 <element name="EFetch-fasta-text-chunk1" ftype="fasta">
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47 <assert_contents>
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48 <has_text text="XM_036034467"/>
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49 <has_text text="NC_040910"/>
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50 </assert_contents>
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51 </element>
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52 </output_collection>
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56 NCBI Entrez EFetch
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57 ==================
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58
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59 Responds to a list of UIDs in a given database with the corresponding data
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60 records in a specified format.
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62 Example Queries
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63 ---------------
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65 Fetch PMIDs 17284678 and 9997 as text abstracts:
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67 +----------------------+--------------------------------------+
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68 | Parameter | Value |
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69 +======================+======================================+
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70 | NCBI Database to Use | PubMed |
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71 +----------------------+--------------------------------------+
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72 | ID List | 17284678 9997 |
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73 +----------------------+--------------------------------------+
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74 | Output Format | Abstract |
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75 +----------------------+--------------------------------------+
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77 Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
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79 +----------------------+--------------------------------------+
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80 | Parameter | Value |
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81 +======================+======================================+
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82 | NCBI Database to Use | Protein |
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83 +----------------------+--------------------------------------+
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84 | ID List | 312836839 34577063 |
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85 +----------------------+--------------------------------------+
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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86 | Output Format | Fasta |
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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87 +----------------------+--------------------------------------+
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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88
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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89 @REFERENCES@
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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90
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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91 @DISCLAIMER@
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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92 ]]></help>
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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93 <expand macro="citations"/>
1b4ac594d02a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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94 </tool>