Mercurial > repos > iuc > ncbi_eutils_efetch

annotate efetch.xml @ 4:c26d1863f3f3 draft

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author iuc
date Fri, 10 Jun 2016 15:03:49 -0400
parents aa88712a7536
children e269b3b5185b
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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 $whole
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23 > $default]]></command>
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24 <inputs>
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25 <expand macro="db"/>
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26 <expand macro="list_or_hist"/>
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27 <param checked="false" label="Download all records associated with query" name="whole" type="boolean" truevalue="--whole" falsevalue=""/>
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28 </inputs>
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29 <outputs>
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30 <data format="txt" name="default" label="NCBI EFetch Results">
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31 <discover_datasets pattern="__designation__.out" ext="txt"/>
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32 <expand macro="efetch_formats" />
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33 </data>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="db_select" value="taxonomy"/>
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38 <param name="output_format" value="full-xml"/>
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39 <param name="qss" value="id_list"/>
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40 <param name="id_list" value="10239"/>
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41 <output name="default" file="viruses.tax.xml">
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42 </output>
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 NCBI Entrez EFetch
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47 ==================
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48
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49 Responds to a list of UIDs in a given database with the corresponding data
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50 records in a specified format.
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51
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52 Example Queries
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53 ---------------
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54
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55 Fetch PMIDs 17284678 and 9997 as text abstracts:
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56
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57 +----------------------+--------------------------------------+
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58 | Parameter | Value |
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59 +======================+======================================+
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60 | NCBI Database to Use | PubMed |
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61 +----------------------+--------------------------------------+
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62 | ID List | 17284678 9997 |
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63 +----------------------+--------------------------------------+
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64 | Output Format | Abstract |
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65 +----------------------+--------------------------------------+
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66
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67 Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
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68
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69 +----------------------+--------------------------------------+
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70 | Parameter | Value |
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71 +======================+======================================+
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72 | NCBI Database to Use | Protein |
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73 +----------------------+--------------------------------------+
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74 | ID List | 312836839 34577063 |
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75 +----------------------+--------------------------------------+
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76 | Output Format | Fasta |
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77 +----------------------+--------------------------------------+
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78
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79 @REFERENCES@
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80
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81 @DISCLAIMER@
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82 ]]></help>
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83 <expand macro="citations"/>
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84 </tool>