Mercurial > repos > iuc > ncbi_eutils_esearch

annotate esearch.xml @ 2:c6096cd97120 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
author iuc
date Wed, 11 Mar 2020 04:03:14 -0400
parents 30150bd36c9a
children e267701c187b
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1 <?xml version="1.0"?>
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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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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"><![CDATA[
c6096cd97120 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
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10 python '$__tool_directory__/esearch.py'
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11 $db_select
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12 "$term"
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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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14 #if $history_file and $history_file is not None:
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15 --history_file '$history_file'
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16 #end if
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17
1
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18 #if $date.enabled == 'True'
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19 --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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21 #if $date.reldate and $date.reldate is not None:
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22 --reldate $date.reldate
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23 #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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25 #if $date.mindate and $date.mindate is not None:
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26 --mindate '$date.mindate'
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27 #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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29 #if $date.maxdate and $date.maxdate is not None:
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30 --maxdate '$date.maxdate'
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31 #end if
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32 #end if
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34 #if $use_history:
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35 --history_out $history
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36 #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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38 @EMAIL_ARGUMENTS@
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39 > $default]]></command>
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40 <inputs>
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41 <expand macro="dbselect"/>
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42 <param name="term" type="text" label="Search term">
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43 <sanitizer>
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44 <valid>
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45 <add value="'"/>
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46 <add value="["/>
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47 <add value="]"/>
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48 </valid>
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49 </sanitizer>
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50 </param>
1
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51 <param name="history_file" type="data" format="json" optional="true" label="Filter existing history" />
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52 <param name="use_history" type="boolean" truevalue="--use_history" falsevalue="" checked="false" label="Store results to history server" />
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53 <conditional name="date">
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54 <param name="enabled" type="select" label="Filter by date">
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55 <option value="False">No</option>
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56 <option value="True">Yes</option>
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57 </param>
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58 <when value="True">
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59 <param label="Date type" name="datetype" type="select">
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60 <option value="PDAT">Publish date</option>
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61 <option value="EDAT">Entrez date</option>
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62 <option value="MDAT">Modification date</option>
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63 </param>
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64 <param name="reldate" type="integer" min="1" optional="true" label="In past N days" />
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65 <param name="mindate" type="text" label="Minimum date" help="YYYY, YYYY/MM or YYYY/MM/DD" />
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66 <param name="maxdate" type="text" label="Maximum date" help="YYYY, YYYY/MM or YYYY/MM/DD" />
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67 </when>
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68 <when value="False"/>
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69 </conditional>
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70 </inputs>
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71 <outputs>
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72 <data name="default" format="json" label="ESearch results for $term">
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73 <change_format>
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74 <when input="use_history" value="" format="xml"/>
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75 </change_format>
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76 </data>
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77 <expand macro="history_out">
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78 <filter>use_history</filter>
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79 </expand>
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="db_select" value="pubmed"/>
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84 <param name="term" value="(PNAS[ta] AND 97[vi])"/>
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85 <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/>
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86 </test>
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87 <test>
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88 <param name="db_select" value="pubmed"/>
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89 <param name="term" value="PNAS[ta]"/>
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90 <param name="enabled" value="True"/>
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91 <param name="datetype" value="PDAT"/>
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92 <param name="mindate" value="2014/01/01"/>
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93 <param name="maxdate" value="2014/02/01"/>
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94 <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/>
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95 </test>
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96 </tests>
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97 <help><![CDATA[
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98 NCBI Entrez ESearch
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99 ===================
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100
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101 Responds to a text query with the list of matching UIDs in a given database
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102 (for later use in ESummary, EFetch or ELink), along with the term translations
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103 of the query.
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104
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105 Example Queries
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106 ---------------
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107
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108 Search in PubMed with the term cancer for abstracts that have an Entrez date
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109 within the last 60 days:
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110
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111 +----------------------+-------------+
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112 | Parameter | Value |
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113 +======================+=============+
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114 | NCBI Database to Use | PubMed |
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115 +----------------------+-------------+
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116 | Term | Cancer |
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117 +----------------------+-------------+
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118 | Datetype | Entrez Date |
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119 +----------------------+-------------+
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120 | In past N Days | 60 |
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121 +----------------------+-------------+
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122
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123 Search PubMed Central for free full text articles containing the query stem cells:
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124
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125 +----------------------+--------------------------------------+
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126 | Parameter | Value |
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127 +======================+======================================+
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128 | NCBI Database to Use | PubMedCentral |
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129 +----------------------+--------------------------------------+
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130 | Term | Stem Cells AND free fulltext[filter] |
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131 +----------------------+--------------------------------------+
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132
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133 Search in Nucleotide for all tRNAs:
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134
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135 +----------------------+--------------------------------------+
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136 | Parameter | Value |
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137 +======================+======================================+
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138 | NCBI Database to Use | Nucleotide |
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139 +----------------------+--------------------------------------+
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140 | Term | biomol trna[prop] |
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141 +----------------------+--------------------------------------+
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142
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143 Search in Protein for a molecular weight range:
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144
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145 +----------------------+--------------------------------------+
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146 | Parameter | Value |
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147 +======================+======================================+
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148 | NCBI Database to Use | Protein |
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149 +----------------------+--------------------------------------+
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150 | Term | 70000:90000[molecular weight] |
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151 +----------------------+--------------------------------------+
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152
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153
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154 @REFERENCES@
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155
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156 @DISCLAIMER@
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157 ]]></help>
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158 <expand macro="citations"/>
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159 </tool>