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comparison efetch.xml @ 0:71bcf87a7031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
author iuc
date Thu, 07 Jul 2016 02:39:36 -0400
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children 0fc65a60436f
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-1:000000000000 0:71bcf87a7031
1 <?xml version="1.0"?>
2 <tool id="ncbi_eutils_efetch" name="NCBI EFetch" version="@WRAPPER_VERSION@">
3 <description>fetch records from NCBI</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <version_command>python efetch.py --version</version_command>
9 <command detect_errors="aggressive" interpreter="python"><![CDATA[efetch.py
10 $db.db_select
11
12 @LIST_OR_HIST@
13
14 #set rettype, retmode = str($db.output_format).split('-')
15 ## Otherwise, defaults to a None/empty which implies 'default' to NCBI
16 #if retmode != "null":
17 --retmode $retmode
18 #end if
19 --rettype $rettype
20
21 @EMAIL_ARGUMENTS@
22 ]]></command>
23 <inputs>
24 <expand macro="db"/>
25 <expand macro="list_or_hist"/>
26 </inputs>
27 <outputs>
28 <collection type="list" label="NCBI EFetch Results" name="output1">
29 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
30 </collection>
31 </outputs>
32 <tests>
33 <test>
34 <param name="db_select" value="taxonomy"/>
35 <param name="output_format" value="full-xml"/>
36 <param name="qss" value="id_list"/>
37 <param name="id_list" value="10239"/>
38 <output name="default">
39 <discovered_dataset designation="EFetch Results Chunk 0" ftype="xml" file="viruses.tax.xml" lines_diff="2">
40 </discovered_dataset>
41 </output>
42 </test>
43 </tests>
44 <help><![CDATA[
45 NCBI Entrez EFetch
46 ==================
47
48 Responds to a list of UIDs in a given database with the corresponding data
49 records in a specified format.
50
51 Example Queries
52 ---------------
53
54 Fetch PMIDs 17284678 and 9997 as text abstracts:
55
56 +----------------------+--------------------------------------+
57 | Parameter | Value |
58 +======================+======================================+
59 | NCBI Database to Use | PubMed |
60 +----------------------+--------------------------------------+
61 | ID List | 17284678 9997 |
62 +----------------------+--------------------------------------+
63 | Output Format | Abstract |
64 +----------------------+--------------------------------------+
65
66 Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
67
68 +----------------------+--------------------------------------+
69 | Parameter | Value |
70 +======================+======================================+
71 | NCBI Database to Use | Protein |
72 +----------------------+--------------------------------------+
73 | ID List | 312836839 34577063 |
74 +----------------------+--------------------------------------+
75 | Output Format | Fasta |
76 +----------------------+--------------------------------------+
77
78 @REFERENCES@
79
80 @DISCLAIMER@
81 ]]></help>
82 <expand macro="citations"/>
83 </tool>