Mercurial > repos > iuc > ncbi_eutils_esearch

annotate 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 f3a84eecaf8b
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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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1 <?xml version="1.0"?>
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2 <tool id="ncbi_eutils_esearch" name="NCBI ESearch" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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3 <description>search NCBI Databases by text query</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <version_command>python esearch.py --version</version_command>
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9 <command detect_errors="aggressive">
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10 <![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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12 ##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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13 #set saniterm = $term.replace('"','\\"')
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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15 python '$__tool_directory__/esearch.py'
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3
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17 $db_select
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19 "$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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21 #if $history_file and $history_file is not None:
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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22 --history_file '$history_file'
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23 #end if
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25 #if $date.enabled == 'True'
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26 --datetype $date.datetype
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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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28 #if $date.reldate and $date.reldate is not None:
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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29 --reldate $date.reldate
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30 #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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32 #if $date.mindate and $date.mindate is not None:
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33 --mindate '$date.mindate'
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34 #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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36 #if $date.maxdate and $date.maxdate is not None:
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37 --maxdate '$date.maxdate'
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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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39 #end if
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3
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41 #if $retstart is not None:
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42 --retstart '$retstart'
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43 #end if
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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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45 #if $retmax is not None:
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46 --retmax '$retmax'
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47 #end if
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48
3
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49 #if $output_format == 'history_xml':
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50 --history_out
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51 --retmode xml
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52 #elif $output_format == 'history_json':
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53 --history_out
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54 --retmode json
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55 #elif $output_format == 'id_xml':
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56 --retmode xml
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57 #elif $output_format == 'id_json':
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58 --retmode json
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59 #elif $output_format == 'id_text':
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60 --retmode text
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61 #end if
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62
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63 @EMAIL_ARGUMENTS@
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64
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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65 > $default
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66
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67 ]]>
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68 </command>
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69 <inputs>
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70 <expand macro="dbselect"/>
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71 <param name="term" type="text" label="Search term">
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72 <sanitizer>
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73 <valid>
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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 <add value='"'/>
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78 </valid>
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79 </sanitizer>
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80 </param>
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81 <param name="history_file" type="data" format="json" optional="true" label="Filter existing history" />
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82 <param name="output_format" type="select" label="Output Format">
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83 <option value="history_json">History File (json)</option>
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84 <option value="history_xml">History File (xml)</option>
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85 <option value="id_xml">ID File (xml)</option>
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86 <option value="id_json">ID File (json)</option>
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87 <option value="id_text" selected="true">ID File (tabular)</option>
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88 </param>
0
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89 <conditional name="date">
1
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90 <param name="enabled" type="select" label="Filter by date">
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91 <option value="False">No</option>
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92 <option value="True">Yes</option>
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93 </param>
0
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94 <when value="True">
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95 <param label="Date type" name="datetype" type="select">
1
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parents: 0
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96 <option value="PDAT">Publish date</option>
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iuc
parents: 0
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97 <option value="EDAT">Entrez date</option>
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98 <option value="MDAT">Modification date</option>
0
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99 </param>
1
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100 <param name="reldate" type="integer" min="1" optional="true" label="In past N days" />
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101 <param name="mindate" type="text" label="Minimum date" help="YYYY, YYYY/MM or YYYY/MM/DD" />
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102 <param name="maxdate" type="text" label="Maximum date" help="YYYY, YYYY/MM or YYYY/MM/DD" />
0
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103 </when>
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104 <when value="False"/>
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105 </conditional>
3
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106 <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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107 <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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108 </inputs>
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109 <outputs>
3
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110 <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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111 <change_format>
3
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112 <when input="output_format" value="history_json" format="json" />
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113 <when input="output_format" value="history_xml" format="xml" />
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114 <when input="output_format" value="id_xml" format="xml" />
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115 <when input="output_format" value="id_json" format="json" />
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116 <when input="output_format" value="id_text" format="tabular" />
0
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117 </change_format>
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118 </data>
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119 </outputs>
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120 <tests>
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121 <test>
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122 <param name="db_select" value="pubmed"/>
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123 <param name="term" value="(PNAS[ta] AND 97[vi])"/>
3
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124 <param name="retstart" value="0"/>
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125 <param name="retmax" value="20"/>
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126 <param name="output_format" value="id_xml"/>
0
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127 <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/>
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128 </test>
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129 <test>
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130 <param name="db_select" value="pubmed"/>
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131 <param name="term" value="PNAS[ta]"/>
3
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132 <param name="retstart" value="0"/>
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133 <param name="retmax" value="20"/>
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134 <param name="output_format" value="id_xml"/>
0
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135 <param name="enabled" value="True"/>
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136 <param name="datetype" value="PDAT"/>
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137 <param name="mindate" value="2014/01/01"/>
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138 <param name="maxdate" value="2014/02/01"/>
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139 <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/>
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140 </test>
3
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141 <test>
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142 <param name="db_select" value="gene"/>
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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])"/>
e267701c187b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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144 <param name="retstart" value="2"/>
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145 <param name="retmax" value="22"/>
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146 <param name="output_format" value="id_text"/>
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147 <output name="default" file="esearch.gene.tabular" ftype="tabular" lines_diff="2"/>
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148 </test>
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149 <test>
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150 <param name="db_select" value="gene"/>
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151 <param name="term" value="118502329"/>
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152 <param name="retstart" value="0"/>
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153 <param name="retmax" value="1"/>
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154 <param name="output_format" value="id_json"/>
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155 <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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156 </test>
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157 <test>
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158 <param name="db_select" value="gene"/>
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159 <param name="term" value="118502329"/>
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160 <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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161 <param name="retmax" value="1"/>
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162 <param name="output_format" value="history_json"/>
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163 <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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164 </test>
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165 <test>
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166 <param name="db_select" value="gene"/>
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167 <param name="term" value="118502329"/>
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168 <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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169 <param name="retmax" value="1"/>
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170 <param name="output_format" value="history_xml"/>
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171 <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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172 </test>
0
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173 </tests>
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174 <help><![CDATA[
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175 NCBI Entrez ESearch
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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
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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178 Responds to a text query with the list of matching UIDs in a given database
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179 (for later use in ESummary, EFetch or ELink), along with the term translations
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180 of the query.
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181
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182 Example Queries
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183 ---------------
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184
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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185 Search in PubMed with the term cancer for abstracts that have an Entrez date
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186 within the last 60 days:
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187
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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188 +----------------------+-------------+
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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189 | Parameter | Value |
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190 +======================+=============+
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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191 | NCBI Database to Use | PubMed |
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192 +----------------------+-------------+
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193 | Term | Cancer |
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194 +----------------------+-------------+
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195 | Datetype | Entrez Date |
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196 +----------------------+-------------+
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197 | In past N Days | 60 |
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198 +----------------------+-------------+
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199
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200 Search PubMed Central for free full text articles containing the query stem cells:
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201
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202 +----------------------+--------------------------------------+
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203 | Parameter | Value |
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204 +======================+======================================+
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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205 | NCBI Database to Use | PubMedCentral |
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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206 +----------------------+--------------------------------------+
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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207 | Term | Stem Cells AND free fulltext[filter] |
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208 +----------------------+--------------------------------------+
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209
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210 Search in Nucleotide for all tRNAs:
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211
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212 +----------------------+--------------------------------------+
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213 | Parameter | Value |
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214 +======================+======================================+
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215 | NCBI Database to Use | Nucleotide |
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216 +----------------------+--------------------------------------+
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217 | Term | biomol trna[prop] |
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218 +----------------------+--------------------------------------+
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219
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220 Search in Protein for a molecular weight range:
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221
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222 +----------------------+--------------------------------------+
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223 | Parameter | Value |
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224 +======================+======================================+
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225 | NCBI Database to Use | Protein |
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226 +----------------------+--------------------------------------+
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227 | Term | 70000:90000[molecular weight] |
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228 +----------------------+--------------------------------------+
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229
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230
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231 @REFERENCES@
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232
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233 @DISCLAIMER@
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234 ]]></help>
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235 <expand macro="citations"/>
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236 </tool>