Mercurial > repos > iuc > ncbi_eutils_esearch

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 851b88d92fa7740880a5edf407f629bf3f7f7bf0
author iuc
date Fri, 04 Oct 2024 14:36:55 +0000
parents e267701c187b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c6096cd97120 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
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1 <tool id="ncbi_eutils_esearch" name="NCBI ESearch" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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2 <description>search NCBI Databases by text query</description>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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3 <macros>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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4 <import>macros.xml</import>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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5 </macros>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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6 <expand macro="requirements"/>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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7 <version_command>python esearch.py --version</version_command>
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8 <command detect_errors="aggressive">
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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9 <![CDATA[
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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11 ##Doing replacement here so that dataset label doesn't have slashes
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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12 #set saniterm = $term.replace('"','\\"')
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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14 python '$__tool_directory__/esearch.py'
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16 $db_select
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18 "$saniterm"
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e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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20 #if $history_file and $history_file is not None:
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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21 --history_file '$history_file'
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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22 #end if
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24 #if $date.enabled == 'True'
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25 --datetype $date.datetype
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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27 #if $date.reldate and $date.reldate is not None:
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28 --reldate $date.reldate
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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29 #end if
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c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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31 #if $date.mindate and $date.mindate is not None:
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32 --mindate '$date.mindate'
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33 #end if
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c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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35 #if $date.maxdate and $date.maxdate is not None:
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36 --maxdate '$date.maxdate'
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37 #end if
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38 #end if
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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40 #if $retstart is not None:
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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41 --retstart '$retstart'
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42 #end if
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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44 #if $retmax is not None:
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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45 --retmax '$retmax'
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46 #end if
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47
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48 #if $output_format == 'history_xml':
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49 --history_out
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50 --retmode xml
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51 #elif $output_format == 'history_json':
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52 --history_out
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53 --retmode json
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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54 #elif $output_format == 'id_xml':
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55 --retmode xml
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56 #elif $output_format == 'id_json':
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57 --retmode json
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58 #elif $output_format == 'id_text':
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59 --retmode text
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60 #end if
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62 @EMAIL_ARGUMENTS@
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e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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64 > $default
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65
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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66 ]]>
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67 </command>
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68 <inputs>
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69 <expand macro="dbselect"/>
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70 <param name="term" type="text" label="Search term">
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71 <sanitizer>
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72 <valid>
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73 <add value="'"/>
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74 <add value="["/>
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75 <add value="]"/>
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76 <add value='"'/>
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77 </valid>
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78 </sanitizer>
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79 </param>
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80 <param name="history_file" type="data" format="json" optional="true" label="Filter existing history" />
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81 <param name="output_format" type="select" label="Output Format">
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82 <option value="history_json">History File (json)</option>
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83 <option value="history_xml">History File (xml)</option>
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84 <option value="id_xml">ID File (xml)</option>
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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85 <option value="id_json">ID File (json)</option>
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86 <option value="id_text" selected="true">ID File (tabular)</option>
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87 </param>
0
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88 <conditional name="date">
1
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89 <param name="enabled" type="select" label="Filter by date">
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90 <option value="False">No</option>
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91 <option value="True">Yes</option>
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92 </param>
0
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93 <when value="True">
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94 <param label="Date type" name="datetype" type="select">
1
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parents: 0
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95 <option value="PDAT">Publish date</option>
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iuc
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96 <option value="EDAT">Entrez date</option>
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iuc
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97 <option value="MDAT">Modification date</option>
0
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98 </param>
1
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99 <param name="reldate" type="integer" min="1" optional="true" label="In past N days" />
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100 <param name="mindate" type="text" label="Minimum date" help="YYYY, YYYY/MM or YYYY/MM/DD" />
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101 <param name="maxdate" type="text" label="Maximum date" help="YYYY, YYYY/MM or YYYY/MM/DD" />
0
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102 </when>
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103 <when value="False"/>
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104 </conditional>
3
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105 <param name="retstart" type="integer" value="0" min="0" max="99999" label="Starting record to return (--retstart)" />
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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106 <param name="retmax" type="integer" value="100000" min="1" max="100000" label="Maximum number of records to return (--retmax)" />
0
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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107 </inputs>
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108 <outputs>
3
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109 <data name="default" format="xml" label="ESearch results for $db_select database query: $term">
0
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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110 <change_format>
3
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111 <when input="output_format" value="history_json" format="json" />
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112 <when input="output_format" value="history_xml" format="xml" />
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113 <when input="output_format" value="id_xml" format="xml" />
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114 <when input="output_format" value="id_json" format="json" />
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115 <when input="output_format" value="id_text" format="tabular" />
0
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116 </change_format>
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117 </data>
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118 </outputs>
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119 <tests>
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120 <test>
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121 <param name="db_select" value="pubmed"/>
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122 <param name="term" value="(PNAS[ta] AND 97[vi])"/>
3
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123 <param name="retstart" value="0"/>
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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124 <param name="retmax" value="20"/>
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125 <param name="output_format" value="id_xml"/>
0
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126 <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/>
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127 </test>
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128 <test>
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129 <param name="db_select" value="pubmed"/>
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130 <param name="term" value="PNAS[ta]"/>
3
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131 <param name="retstart" value="0"/>
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132 <param name="retmax" value="20"/>
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133 <param name="output_format" value="id_xml"/>
0
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134 <param name="enabled" value="True"/>
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135 <param name="datetype" value="PDAT"/>
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136 <param name="mindate" value="2014/01/01"/>
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137 <param name="maxdate" value="2014/02/01"/>
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138 <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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139 </test>
3
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140 <test>
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141 <param name="db_select" value="gene"/>
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142 <param name="term" value="&quot;genetype rrna&quot;[Properties] AND &quot;Homo sapiens&quot;[Organism] AND (&quot;srcdb refseq&quot;[Properties] AND alive[prop])"/>
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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143 <param name="retstart" value="2"/>
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144 <param name="retmax" value="22"/>
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145 <param name="output_format" value="id_text"/>
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146 <output name="default" file="esearch.gene.tabular" ftype="tabular" lines_diff="2"/>
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147 </test>
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148 <test>
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149 <param name="db_select" value="gene"/>
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150 <param name="term" value="118502329"/>
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151 <param name="retstart" value="0"/>
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152 <param name="retmax" value="1"/>
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153 <param name="output_format" value="id_json"/>
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154 <output name="default" file="esearch.gene.json" ftype="json" lines_diff="2"/>
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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155 </test>
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156 <test>
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157 <param name="db_select" value="gene"/>
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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158 <param name="term" value="118502329"/>
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159 <param name="retstart" value="0"/>
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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160 <param name="retmax" value="1"/>
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161 <param name="output_format" value="history_json"/>
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162 <output name="default" file="esearch.gene.hist.json" ftype="json" lines_diff="2"/>
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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163 </test>
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164 <test>
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165 <param name="db_select" value="gene"/>
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166 <param name="term" value="118502329"/>
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167 <param name="retstart" value="0"/>
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168 <param name="retmax" value="1"/>
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169 <param name="output_format" value="history_xml"/>
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170 <output name="default" file="esearch.gene.hist.xml" ftype="xml" lines_diff="2"/>
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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171 </test>
0
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172 </tests>
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173 <help><![CDATA[
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174 NCBI Entrez ESearch
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175 ===================
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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176
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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177 Responds to a text query with the list of matching UIDs in a given database
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178 (for later use in ESummary, EFetch or ELink), along with the term translations
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179 of the query.
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180
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181 Example Queries
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182 ---------------
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183
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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184 Search in PubMed with the term cancer for abstracts that have an Entrez date
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185 within the last 60 days:
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186
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187 +----------------------+-------------+
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188 | Parameter | Value |
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189 +======================+=============+
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190 | NCBI Database to Use | PubMed |
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191 +----------------------+-------------+
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192 | Term | Cancer |
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193 +----------------------+-------------+
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194 | Datetype | Entrez Date |
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195 +----------------------+-------------+
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196 | In past N Days | 60 |
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197 +----------------------+-------------+
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198
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199 Search PubMed Central for free full text articles containing the query stem cells:
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200
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201 +----------------------+--------------------------------------+
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202 | Parameter | Value |
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203 +======================+======================================+
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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204 | NCBI Database to Use | PubMedCentral |
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205 +----------------------+--------------------------------------+
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206 | Term | Stem Cells AND free fulltext[filter] |
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207 +----------------------+--------------------------------------+
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208
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209 Search in Nucleotide for all tRNAs:
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210
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211 +----------------------+--------------------------------------+
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212 | Parameter | Value |
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213 +======================+======================================+
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214 | NCBI Database to Use | Nucleotide |
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215 +----------------------+--------------------------------------+
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216 | Term | biomol trna[prop] |
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217 +----------------------+--------------------------------------+
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218
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219 Search in Protein for a molecular weight range:
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220
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221 +----------------------+--------------------------------------+
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222 | Parameter | Value |
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223 +======================+======================================+
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224 | NCBI Database to Use | Protein |
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225 +----------------------+--------------------------------------+
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226 | Term | 70000:90000[molecular weight] |
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227 +----------------------+--------------------------------------+
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228
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229
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230 @REFERENCES@
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231
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232 @DISCLAIMER@
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233 ]]></help>
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234 <expand macro="citations"/>
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235 </tool>