Mercurial > repos > iuc > ncbi_eutils_efetch

comparison efetch.xml @ 0:1b4ac594d02a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
author iuc
date Sat, 31 Oct 2015 12:44:54 -0400
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-1:000000000000 0:1b4ac594d02a
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 <expand macro="stdio"/>
9 <version_command>python efetch.py --version</version_command>
10 <command interpreter="python"><![CDATA[efetch.py
11 $db.db_select
12
13 @LIST_OR_HIST@
14
15 #set retmode, rettype = str($db.output_format).split('-')
16 ## Otherwise, defaults to a None/empty which implies 'default' to NCBI
17 #if retmode != "null":
18 --retmode $retmode
19 #end if
20 --rettype $rettype
21
22 @EMAIL_ARGUMENTS@
23 $whole
24 > $default]]></command>
25 <inputs>
26 <expand macro="db"/>
27 <expand macro="list_or_hist"/>
28 <param checked="false" label="Download all records associated with query" name="whole" type="boolean" truevalue="--whole" falsevalue=""/>
29 </inputs>
30 <outputs>
31 <data format="txt" name="default" label="NCBI EFetch Results">
32 <discover_datasets pattern="__designation__.out" ext="txt"/>
33 <change_format>
34 <when input="output_format" value="abstract-text" format="txt"/>
35 <when input="output_format" value="acc-text" format="txt"/>
36 <when input="output_format" value="alignmentscores-text" format="txt"/>
37 <when input="output_format" value="chr-text" format="txt"/>
38 <when input="output_format" value="docset-text" format="txt"/>
39 <when input="output_format" value="docsum-xml" format="xml"/>
40 <when input="output_format" value="est-text" format="txt"/>
41 <when input="output_format" value="fasta_cds_aa-text" format="fasta"/>
42 <when input="output_format" value="fasta-text" format="fasta"/>
43 <when input="output_format" value="fasta-xml" format="xml"/>
44 <when input="output_format" value="flt-text" format="txt"/>
45 <when input="output_format" value="ft-text" format="txt"/>
46 <when input="output_format" value="full-text" format="txt"/>
47 <when input="output_format" value="full-xml" format="xml"/>
48 <when input="output_format" value="gbc-xml" format="xml"/>
49 <when input="output_format" value="gbwithparts-text" format="genbank"/>
50 <when input="output_format" value="gb-text" format="genbank"/>
51 <when input="output_format" value="gb-xml" format="xml"/>
52 <when input="output_format" value="gene_table-text" format="txt"/>
53 <when input="output_format" value="gpc-xml" format="xml"/>
54 <when input="output_format" value="gp-text" format="txt"/>
55 <when input="output_format" value="gp-xml" format="xml"/>
56 <when input="output_format" value="gss-text" format="txt"/>
57 <when input="output_format" value="homologene-text" format="txt"/>
58 <when input="output_format" value="ipg-xml" format="xml"/>
59 <when input="output_format" value="medline-text" format="txt"/>
60 <when input="output_format" value="native-xml" format="xml"/>
61 <when input="output_format" value="null-asn.1" format="asn1"/>
62 <when input="output_format" value="null-text" format="txt"/>
63 <when input="output_format" value="null-xml" format="xml"/>
64 <when input="output_format" value="rsr-text" format="txt"/>
65 <when input="output_format" value="seqid-text" format="txt"/>
66 <when input="output_format" value="ssexemplar-text" format="txt"/>
67 <when input="output_format" value="summary-text" format="txt"/>
68 <when input="output_format" value="uilist-xml" format="xml"/>
69 <when input="output_format" value="xml-xml" format="xml"/>
70 </change_format>
71 </data>
72 </outputs>
73 <tests>
74 <test>
75 <param name="db_select" value="taxonomy"/>
76 <param name="output_format" value="docsum-xml"/>
77 <param name="qss" value="id_list"/>
78 <param name="id_list" value="10239"/>
79 <output name="default" file="viruses.tax.xml">
80 <!--<discovered_datasets designation="0" ftytpe="xml" file="viruses.tax.xml" />-->
81 </output>
82 </test>
83 </tests>
84 <help><![CDATA[
85 NCBI Entrez EFetch
86 ==================
87
88 Responds to a list of UIDs in a given database with the corresponding data
89 records in a specified format.
90
91 Example Queries
92 ---------------
93
94 Fetch PMIDs 17284678 and 9997 as text abstracts:
95
96 +----------------------+--------------------------------------+
97 | Parameter | Value |
98 +======================+======================================+
99 | NCBI Database to Use | PubMed |
100 +----------------------+--------------------------------------+
101 | ID List | 17284678 9997 |
102 +----------------------+--------------------------------------+
103 | Output Format | Abstract |
104 +----------------------+--------------------------------------+
105
106 Fetch FASTA for a transcript and its protein product (GIs 312836839 and 34577063)
107
108 +----------------------+--------------------------------------+
109 | Parameter | Value |
110 +======================+======================================+
111 | NCBI Database to Use | Protein |
112 +----------------------+--------------------------------------+
113 | ID List | 312836839 34577063 |
114 +----------------------+--------------------------------------+
115 | Output Format | Fasta |
116 +----------------------+--------------------------------------+
117
118 @REFERENCES@
119
120 @DISCLAIMER@
121 ]]></help>
122 <expand macro="citations"/>
123 </tool>