Mercurial > repos > iuc > ncbi_eutils_efetch

annotate efetch.xml @ 5:e269b3b5185b draft

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author iuc
date Thu, 07 Jul 2016 02:37:49 -0400
parents c26d1863f3f3
children 2ff5369b4b51
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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@">
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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" interpreter="python"><![CDATA[efetch.py
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10 $db.db_select
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12 @LIST_OR_HIST@
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13
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14 #set rettype, retmode = str($db.output_format).split('-')
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15 ## Otherwise, defaults to a None/empty which implies 'default' to NCBI
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16 #if retmode != "null":
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17 --retmode $retmode
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18 #end if
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19 --rettype $rettype
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21 @EMAIL_ARGUMENTS@
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22 ]]></command>
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23 <inputs>
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24 <expand macro="db"/>
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25 <expand macro="list_or_hist"/>
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26 </inputs>
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27 <outputs>
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28 <collection type="list" label="NCBI EFetch Results" name="output1">
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29 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
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30 </collection>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="db_select" value="taxonomy"/>
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35 <param name="output_format" value="full-xml"/>
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36 <param name="qss" value="id_list"/>
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37 <param name="id_list" value="10239"/>
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38 <output name="default">
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39 <discovered_dataset designation="EFetch Results Chunk 0" ftype="xml" file="viruses.tax.xml" lines_diff="2">
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40 </discovered_dataset>
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41 </output>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 NCBI Entrez EFetch
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46 ==================
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48 Responds to a list of UIDs in a given database with the corresponding data
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49 records in a specified format.
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51 Example Queries
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52 ---------------
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54 Fetch PMIDs 17284678 and 9997 as text abstracts:
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56 +----------------------+--------------------------------------+
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57 | Parameter | Value |
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58 +======================+======================================+
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59 | NCBI Database to Use | PubMed |
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60 +----------------------+--------------------------------------+
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61 | ID List | 17284678 9997 |
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62 +----------------------+--------------------------------------+
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63 | Output Format | Abstract |
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64 +----------------------+--------------------------------------+
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65
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66 Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
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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 | Protein |
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72 +----------------------+--------------------------------------+
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73 | ID List | 312836839 34577063 |
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74 +----------------------+--------------------------------------+
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75 | Output Format | Fasta |
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76 +----------------------+--------------------------------------+
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78 @REFERENCES@
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80 @DISCLAIMER@
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81 ]]></help>
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82 <expand macro="citations"/>
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83 </tool>