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comparison esearch.xml @ 0:c8a84e910e6b 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 02:40:48 -0400
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children 30150bd36c9a
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-1:000000000000 0:c8a84e910e6b
1 <?xml version="1.0"?>
2 <tool id="ncbi_eutils_esearch" name="NCBI ESearch" version="@WRAPPER_VERSION@">
3 <description>search NCBI Databases by text query</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <version_command>python esearch.py --version</version_command>
9 <command detect_errors="aggressive" interpreter="python"><![CDATA[esearch.py
10 $db_select
11 "$term"
12
13 #if $history_file and $history_file is not None:
14 --history_file $history_file
15 #end if
16
17 #if $date.enabled:
18 --datetype $date.datetype
19
20 #if $date.reldate and $date.reldate is not None:
21 --reldate $date.reldate
22 #end if
23
24 #if $date.mindate and $date.mindate is not None:
25 --mindate $date.mindate
26 #end if
27
28 #if $date.maxdate and $date.maxdate is not None:
29 --maxdate $date.maxdate
30 #end if
31 #end if
32
33 #if $use_history:
34 --history_out $history
35 #end if
36
37 @EMAIL_ARGUMENTS@
38 > $default]]></command>
39 <inputs>
40 <expand macro="dbselect"/>
41 <param label="Search Term" name="term" type="text">
42 <sanitizer>
43 <valid>
44 <add value="'"/>
45 <add value="["/>
46 <add value="]"/>
47 </valid>
48 </sanitizer>
49 </param>
50 <param label="Filter existing history" name="history_file" type="data" format="json" optional="True"/>
51 <param checked="false" label="Store results to history server" name="use_history" type="boolean" truevalue="--use_history" falsevalue=""/>
52 <conditional name="date">
53 <param label="Filter By Date" type="boolean" truevalue="True" falsevalue="False" checked="false" name="enabled"/>
54 <when value="True">
55 <param label="Date type" name="datetype" type="select">
56 <option value="PDAT">Publish Date</option>
57 <option value="EDAT">Entrez Date</option>
58 <option value="MDAT">Modification Date</option>
59 </param>
60 <param label="In past N days" name="reldate" type="integer" min="1" optional="True"/>
61 <param label="Minimum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="mindate" type="text"/>
62 <param label="maximum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="maxdate" type="text"/>
63 </when>
64 <when value="False"/>
65 </conditional>
66 </inputs>
67 <outputs>
68 <data format="json" name="default" label="ESearch Results for $term">
69 <change_format>
70 <when input="use_history" value="" format="xml"/>
71 </change_format>
72 </data>
73 <expand macro="history_out">
74 <filter>use_history</filter>
75 </expand>
76 </outputs>
77 <tests>
78 <test>
79 <param name="db_select" value="pubmed"/>
80 <param name="term" value="(PNAS[ta] AND 97[vi])"/>
81 <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/>
82 </test>
83 <test>
84 <param name="db_select" value="pubmed"/>
85 <param name="term" value="PNAS[ta]"/>
86 <param name="enabled" value="True"/>
87 <param name="datetype" value="PDAT"/>
88 <param name="mindate" value="2014/01/01"/>
89 <param name="maxdate" value="2014/02/01"/>
90 <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/>
91 </test>
92 </tests>
93 <help><![CDATA[
94 NCBI Entrez ESearch
95 ===================
96
97 Responds to a text query with the list of matching UIDs in a given database
98 (for later use in ESummary, EFetch or ELink), along with the term translations
99 of the query.
100
101 Example Queries
102 ---------------
103
104 Search in PubMed with the term cancer for abstracts that have an Entrez date
105 within the last 60 days:
106
107 +----------------------+-------------+
108 | Parameter | Value |
109 +======================+=============+
110 | NCBI Database to Use | PubMed |
111 +----------------------+-------------+
112 | Term | Cancer |
113 +----------------------+-------------+
114 | Datetype | Entrez Date |
115 +----------------------+-------------+
116 | In past N Days | 60 |
117 +----------------------+-------------+
118
119 Search PubMed Central for free full text articles containing the query stem cells:
120
121 +----------------------+--------------------------------------+
122 | Parameter | Value |
123 +======================+======================================+
124 | NCBI Database to Use | PubMedCentral |
125 +----------------------+--------------------------------------+
126 | Term | Stem Cells AND free fulltext[filter] |
127 +----------------------+--------------------------------------+
128
129 Search in Nucleotide for all tRNAs:
130
131 +----------------------+--------------------------------------+
132 | Parameter | Value |
133 +======================+======================================+
134 | NCBI Database to Use | Nucleotide |
135 +----------------------+--------------------------------------+
136 | Term | biomol trna[prop] |
137 +----------------------+--------------------------------------+
138
139 Search in Protein for a molecular weight range:
140
141 +----------------------+--------------------------------------+
142 | Parameter | Value |
143 +======================+======================================+
144 | NCBI Database to Use | Protein |
145 +----------------------+--------------------------------------+
146 | Term | 70000:90000[molecular weight] |
147 +----------------------+--------------------------------------+
148
149
150 @REFERENCES@
151
152 @DISCLAIMER@
153 ]]></help>
154 <expand macro="citations"/>
155 </tool>