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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 02:39:21 -0400
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1 <?xml version="1.0"?>
2 <tool id="ncbi_eutils_ecitmatch" name="NCBI ECitMatch" version="@WRAPPER_VERSION@">
3 <description>search NCBI for citations in PubMed</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <version_command>python ecitmatch.py --version</version_command>
9 <command detect_errors="aggressive" interpreter="python"><![CDATA[ecitmatch.py
10
11 #if str($input.method) == "file":
12 --file $input.citation_file
13 #else
14 #set keys = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
15 #set journal_title = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
16 #set year = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
17 #set volume = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
18 #set first_page = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
19 #set author = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
20
21 --key "$keys"
22 --journal_title "$journal_title"
23 --key "$year"
24 --key "$volume"
25 --key "$first_page"
26 --key "$author"
27 #end if
28
29 @EMAIL_ARGUMENTS@
30 > $default]]></command>
31 <inputs>
32 <conditional name="input">
33 <param name="method" type="select" label="Input method">
34 <option value="file">Load citations from a formatted table</option>
35 <option value="direct">Direct Input</option>
36 </param>
37 <when value="file">
38 <param label="Citation table" name="citation_file" type="data"
39 format="tabular" help="Columns must be in a specific order, see help documentation"/>
40 </when>
41 <when value="direct">
42 <repeat name="citations" title="Citations">
43 <param name="journal_title" type="text" label="Journal Title"
44 help="E.g. proc natl acad sci u s a" />
45 <param name="year" type="integer" label="Year" value="2000"/>
46 <param name="volume" type="integer" label="Volume" value="88"/>
47 <param name="first_page" type="integer" label="First Page" value="1"/>
48 <param name="author" type="text" label="Author's Name" />
49 <param name="key" type="text" label="Citation key"
50 help="Used to match input results to NCBI's output" />
51 </repeat>
52 </when>
53 </conditional>
54
55 </inputs>
56 <outputs>
57 <data format="tabular" name="default" label="ECitMatch Results"/>
58 </outputs>
59 <tests>
60 <test>
61 <param name="method" value="file"/>
62 <param name="citation_file" value="ecitmatch.tsv"/>
63 <output name="default" file="ecitmatch.results.tsv" ftype="tabular"/>
64 </test>
65 </tests>
66 <help><![CDATA[
67 NCBI ECitMatch
68 ==============
69
70 Search for citation PubMed IDs. These can be provided via a tabular file, or
71 via direct input. If provided via file, the columns should be ordered:
72
73 1. Journal Name
74 2. Year
75 3. Volume
76 4. First Page
77 5. Author Name
78 6. Citation Key
79
80
81 An example query:
82
83 +---------------+--------------------------+
84 | Parameter | Value |
85 +===============+==========================+
86 | Journal Title | proc natl acad sci u s a |
87 +---------------+--------------------------+
88 | Year | 1991 |
89 +---------------+--------------------------+
90 | Volume | 88 |
91 +---------------+--------------------------+
92 | First Page | 3248 |
93 +---------------+--------------------------+
94 | Author Name | mann bj |
95 +---------------+--------------------------+
96 | Citation Key | citation_1 |
97 +---------------+--------------------------+
98
99
100 @REFERENCES@
101
102 @DISCLAIMER@
103 ]]></help>
104 <expand macro="citations"/>
105 </tool>