Mercurial > repos > iuc > ncbi_eutils_esearch

comparison esearch.xml @ 3:e267701c187b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
author iuc
date Wed, 23 Sep 2020 09:48:26 +0000
parents c6096cd97120
children
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2:c6096cd97120 3:e267701c187b
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <version_command>python esearch.py --version</version_command> 8 <version_command>python esearch.py --version</version_command>
9 <command detect_errors="aggressive"><![CDATA[ 9 <command detect_errors="aggressive">
10 python '$__tool_directory__/esearch.py' 10 <![CDATA[
11 $db_select 11
12 "$term" 12 ##Doing replacement here so that dataset label doesn't have slashes
13 13 #set saniterm = $term.replace('"','\\"')
14 #if $history_file and $history_file is not None: 14
15 --history_file '$history_file' 15 python '$__tool_directory__/esearch.py'
16 #end if 16
17 $db_select
18
19 "$saniterm"
20
21 #if $history_file and $history_file is not None:
22 --history_file '$history_file'
23 #end if
17 24
18 #if $date.enabled == 'True' 25 #if $date.enabled == 'True'
19 --datetype $date.datetype 26 --datetype $date.datetype
20 27
21 #if $date.reldate and $date.reldate is not None: 28 #if $date.reldate and $date.reldate is not None:
29 #if $date.maxdate and $date.maxdate is not None: 36 #if $date.maxdate and $date.maxdate is not None:
30 --maxdate '$date.maxdate' 37 --maxdate '$date.maxdate'
31 #end if 38 #end if
32 #end if 39 #end if
33 40
34 #if $use_history: 41 #if $retstart is not None:
35 --history_out $history 42 --retstart '$retstart'
36 #end if 43 #end if
37 44
38 @EMAIL_ARGUMENTS@ 45 #if $retmax is not None:
39 > $default]]></command> 46 --retmax '$retmax'
47 #end if
48
49 #if $output_format == 'history_xml':
50 --history_out
51 --retmode xml
52 #elif $output_format == 'history_json':
53 --history_out
54 --retmode json
55 #elif $output_format == 'id_xml':
56 --retmode xml
57 #elif $output_format == 'id_json':
58 --retmode json
59 #elif $output_format == 'id_text':
60 --retmode text
61 #end if
62
63 @EMAIL_ARGUMENTS@
64
65 > $default
66
67 ]]>
68 </command>
40 <inputs> 69 <inputs>
41 <expand macro="dbselect"/> 70 <expand macro="dbselect"/>
42 <param name="term" type="text" label="Search term"> 71 <param name="term" type="text" label="Search term">
43 <sanitizer> 72 <sanitizer>
44 <valid> 73 <valid>
45 <add value="'"/> 74 <add value="'"/>
46 <add value="["/> 75 <add value="["/>
47 <add value="]"/> 76 <add value="]"/>
77 <add value='"'/>
48 </valid> 78 </valid>
49 </sanitizer> 79 </sanitizer>
50 </param> 80 </param>
51 <param name="history_file" type="data" format="json" optional="true" label="Filter existing history" /> 81 <param name="history_file" type="data" format="json" optional="true" label="Filter existing history" />
52 <param name="use_history" type="boolean" truevalue="--use_history" falsevalue="" checked="false" label="Store results to history server" /> 82 <param name="output_format" type="select" label="Output Format">
83 <option value="history_json">History File (json)</option>
84 <option value="history_xml">History File (xml)</option>
85 <option value="id_xml">ID File (xml)</option>
86 <option value="id_json">ID File (json)</option>
87 <option value="id_text" selected="true">ID File (tabular)</option>
88 </param>
53 <conditional name="date"> 89 <conditional name="date">
54 <param name="enabled" type="select" label="Filter by date"> 90 <param name="enabled" type="select" label="Filter by date">
55 <option value="False">No</option> 91 <option value="False">No</option>
56 <option value="True">Yes</option> 92 <option value="True">Yes</option>
57 </param> 93 </param>
65 <param name="mindate" type="text" label="Minimum date" help="YYYY, YYYY/MM or YYYY/MM/DD" /> 101 <param name="mindate" type="text" label="Minimum date" help="YYYY, YYYY/MM or YYYY/MM/DD" />
66 <param name="maxdate" type="text" label="Maximum date" help="YYYY, YYYY/MM or YYYY/MM/DD" /> 102 <param name="maxdate" type="text" label="Maximum date" help="YYYY, YYYY/MM or YYYY/MM/DD" />
67 </when> 103 </when>
68 <when value="False"/> 104 <when value="False"/>
69 </conditional> 105 </conditional>
106 <param name="retstart" type="integer" value="0" min="0" max="99999" label="Starting record to return (--retstart)" />
107 <param name="retmax" type="integer" value="100000" min="1" max="100000" label="Maximum number of records to return (--retmax)" />
70 </inputs> 108 </inputs>
71 <outputs> 109 <outputs>
72 <data name="default" format="json" label="ESearch results for $term"> 110 <data name="default" format="xml" label="ESearch results for $db_select database query: $term">
73 <change_format> 111 <change_format>
74 <when input="use_history" value="" format="xml"/> 112 <when input="output_format" value="history_json" format="json" />
113 <when input="output_format" value="history_xml" format="xml" />
114 <when input="output_format" value="id_xml" format="xml" />
115 <when input="output_format" value="id_json" format="json" />
116 <when input="output_format" value="id_text" format="tabular" />
75 </change_format> 117 </change_format>
76 </data> 118 </data>
77 <expand macro="history_out">
78 <filter>use_history</filter>
79 </expand>
80 </outputs> 119 </outputs>
81 <tests> 120 <tests>
82 <test> 121 <test>
83 <param name="db_select" value="pubmed"/> 122 <param name="db_select" value="pubmed"/>
84 <param name="term" value="(PNAS[ta] AND 97[vi])"/> 123 <param name="term" value="(PNAS[ta] AND 97[vi])"/>
124 <param name="retstart" value="0"/>
125 <param name="retmax" value="20"/>
126 <param name="output_format" value="id_xml"/>
85 <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/> 127 <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/>
86 </test> 128 </test>
87 <test> 129 <test>
88 <param name="db_select" value="pubmed"/> 130 <param name="db_select" value="pubmed"/>
89 <param name="term" value="PNAS[ta]"/> 131 <param name="term" value="PNAS[ta]"/>
132 <param name="retstart" value="0"/>
133 <param name="retmax" value="20"/>
134 <param name="output_format" value="id_xml"/>
90 <param name="enabled" value="True"/> 135 <param name="enabled" value="True"/>
91 <param name="datetype" value="PDAT"/> 136 <param name="datetype" value="PDAT"/>
92 <param name="mindate" value="2014/01/01"/> 137 <param name="mindate" value="2014/01/01"/>
93 <param name="maxdate" value="2014/02/01"/> 138 <param name="maxdate" value="2014/02/01"/>
94 <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/> 139 <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/>
95 </test> 140 </test>
141 <test>
142 <param name="db_select" value="gene"/>
143 <param name="term" value="&quot;genetype rrna&quot;[Properties] AND &quot;Homo sapiens&quot;[Organism] AND (&quot;srcdb refseq&quot;[Properties] AND alive[prop])"/>
144 <param name="retstart" value="2"/>
145 <param name="retmax" value="22"/>
146 <param name="output_format" value="id_text"/>
147 <output name="default" file="esearch.gene.tabular" ftype="tabular" lines_diff="2"/>
148 </test>
149 <test>
150 <param name="db_select" value="gene"/>
151 <param name="term" value="118502329"/>
152 <param name="retstart" value="0"/>
153 <param name="retmax" value="1"/>
154 <param name="output_format" value="id_json"/>
155 <output name="default" file="esearch.gene.json" ftype="json" lines_diff="2"/>
156 </test>
157 <test>
158 <param name="db_select" value="gene"/>
159 <param name="term" value="118502329"/>
160 <param name="retstart" value="0"/>
161 <param name="retmax" value="1"/>
162 <param name="output_format" value="history_json"/>
163 <output name="default" file="esearch.gene.hist.json" ftype="json" lines_diff="2"/>
164 </test>
165 <test>
166 <param name="db_select" value="gene"/>
167 <param name="term" value="118502329"/>
168 <param name="retstart" value="0"/>
169 <param name="retmax" value="1"/>
170 <param name="output_format" value="history_xml"/>
171 <output name="default" file="esearch.gene.hist.xml" ftype="xml" lines_diff="2"/>
172 </test>
96 </tests> 173 </tests>
97 <help><![CDATA[ 174 <help><![CDATA[
98 NCBI Entrez ESearch 175 NCBI Entrez ESearch
99 =================== 176 ===================
100 177