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comparison ecitmatch.xml @ 0:f1590b9068bd 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 12:44:17 -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 <expand macro="stdio"/>
9 <version_command>python ecitmatch.py --version</version_command>
10 <command interpreter="python"><![CDATA[ecitmatch.py
11
12 #if str($input.method) == "file":
13 --file $input.citation_file
14 #else
15 #set keys = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
16 #set journal_title = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
17 #set year = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
18 #set volume = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
19 #set first_page = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
20 #set author = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
21
22 --key "$keys"
23 --journal_title "$journal_title"
24 --key "$year"
25 --key "$volume"
26 --key "$first_page"
27 --key "$author"
28 #end if
29
30 @EMAIL_ARGUMENTS@
31 > $default]]></command>
32 <inputs>
33 <conditional name="input">
34 <param name="method" type="select" label="Input method">
35 <option value="file">Load citations from a formatted table</option>
36 <option value="direct">Direct Input</option>
37 </param>
38 <when value="file">
39 <param label="Citation table" name="citation_file" type="data"
40 format="tabular" optional="True" help="Columns must be in a specific order, see help documentation"/>
41 </when>
42 <when value="direct">
43 <repeat name="citations" title="Citations">
44 <param name="journal_title" type="text" label="Journal Title"
45 help="E.g. proc natl acad sci u s a" />
46 <param name="year" type="integer" label="Year" value="2000"/>
47 <param name="volume" type="integer" label="Volume" value="88"/>
48 <param name="first_page" type="integer" label="First Page" value="1"/>
49 <param name="author" type="text" label="Author's Name" />
50 <param name="key" type="text" label="Citation key"
51 help="Used to match input results to NCBI's output" />
52 </repeat>
53 </when>
54 </conditional>
55
56 </inputs>
57 <outputs>
58 <data format="tabular" name="default" label="ECitMatch Results"/>
59 </outputs>
60 <tests>
61 <test>
62 <param name="method" value="file"/>
63 <param name="citation_file" value="ecitmatch.tsv"/>
64 <output name="default" file="ecitmatch.results.tsv" />
65 </test>
66 </tests>
67 <help><![CDATA[
68 NCBI ECitMatch
69 ==============
70
71 Search for citation PubMed IDs. These can be provided via a tabular file, or
72 via direct input. If provided via file, the columns should be ordered:
73
74 1. Journal Name
75 2. Year
76 3. Volume
77 4. First Page
78 5. Author Name
79 6. Citation Key
80
81
82 An example query:
83
84 +---------------+--------------------------+
85 | Parameter | Value |
86 +===============+==========================+
87 | Journal Title | proc natl acad sci u s a |
88 +---------------+--------------------------+
89 | Year | 1991 |
90 +---------------+--------------------------+
91 | Volume | 88 |
92 +---------------+--------------------------+
93 | First Page | 3248 |
94 +---------------+--------------------------+
95 | Author Name | mann bj |
96 +---------------+--------------------------+
97 | Citation Key | citation_1 |
98 +---------------+--------------------------+
99
100
101 @REFERENCES@
102
103 @DISCLAIMER@
104 ]]></help>
105 <expand macro="citations"/>
106 </tool>