Mercurial > repos > iuc > ncbi_eutils_esearch

annotate esearch.xml @ 0:c8a84e910e6b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children 30150bd36c9a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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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"?>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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2 <tool id="ncbi_eutils_esearch" name="NCBI ESearch" version="@WRAPPER_VERSION@">
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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3 <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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4 <macros>
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5 <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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6 </macros>
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7 <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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8 <version_command>python esearch.py --version</version_command>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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9 <command detect_errors="aggressive" interpreter="python"><![CDATA[esearch.py
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10 $db_select
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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11 "$term"
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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13 #if $history_file and $history_file 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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14 --history_file $history_file
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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15 #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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17 #if $date.enabled:
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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18 --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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20 #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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21 --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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22 #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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24 #if $date.mindate and $date.mindate 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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25 --mindate $date.mindate
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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26 #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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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.maxdate and $date.maxdate 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 --maxdate $date.maxdate
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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30 #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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31 #end if
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32
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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33 #if $use_history:
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34 --history_out $history
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35 #end if
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36
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37 @EMAIL_ARGUMENTS@
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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38 > $default]]></command>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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39 <inputs>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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40 <expand macro="dbselect"/>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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41 <param label="Search Term" name="term" type="text">
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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42 <sanitizer>
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43 <valid>
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44 <add value="'"/>
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45 <add value="["/>
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46 <add value="]"/>
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47 </valid>
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48 </sanitizer>
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49 </param>
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50 <param label="Filter existing history" name="history_file" type="data" format="json" optional="True"/>
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51 <param checked="false" label="Store results to history server" name="use_history" type="boolean" truevalue="--use_history" falsevalue=""/>
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52 <conditional name="date">
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53 <param label="Filter By Date" type="boolean" truevalue="True" falsevalue="False" checked="false" name="enabled"/>
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54 <when value="True">
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55 <param label="Date type" name="datetype" type="select">
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56 <option value="PDAT">Publish Date</option>
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57 <option value="EDAT">Entrez Date</option>
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58 <option value="MDAT">Modification Date</option>
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59 </param>
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60 <param label="In past N days" name="reldate" type="integer" min="1" optional="True"/>
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61 <param label="Minimum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="mindate" type="text"/>
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62 <param label="maximum date" help="YYYY, YYYY/MM, or YYYY/MM/DD" name="maxdate" type="text"/>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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63 </when>
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64 <when value="False"/>
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65 </conditional>
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66 </inputs>
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67 <outputs>
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68 <data format="json" name="default" label="ESearch Results for $term">
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69 <change_format>
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70 <when input="use_history" value="" format="xml"/>
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71 </change_format>
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72 </data>
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73 <expand macro="history_out">
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74 <filter>use_history</filter>
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75 </expand>
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="db_select" value="pubmed"/>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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80 <param name="term" value="(PNAS[ta] AND 97[vi])"/>
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81 <output name="default" file="esearch.pubmed.xml" ftype="xml" lines_diff="2"/>
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82 </test>
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83 <test>
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84 <param name="db_select" value="pubmed"/>
c8a84e910e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 15bcc5104c577b4b9c761f2854fc686c07ffa9db
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85 <param name="term" value="PNAS[ta]"/>
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86 <param name="enabled" value="True"/>
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87 <param name="datetype" value="PDAT"/>
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88 <param name="mindate" value="2014/01/01"/>
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89 <param name="maxdate" value="2014/02/01"/>
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90 <output name="default" file="esearch.pubmed.2014-01-pnas.xml" ftype="xml" lines_diff="2"/>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 NCBI Entrez ESearch
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95 ===================
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96
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97 Responds to a text query with the list of matching UIDs in a given database
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98 (for later use in ESummary, EFetch or ELink), along with the term translations
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99 of the query.
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100
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101 Example Queries
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102 ---------------
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103
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104 Search in PubMed with the term cancer for abstracts that have an Entrez date
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105 within the last 60 days:
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106
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107 +----------------------+-------------+
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108 | Parameter | Value |
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109 +======================+=============+
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110 | NCBI Database to Use | PubMed |
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111 +----------------------+-------------+
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112 | Term | Cancer |
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113 +----------------------+-------------+
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114 | Datetype | Entrez Date |
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115 +----------------------+-------------+
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116 | In past N Days | 60 |
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117 +----------------------+-------------+
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118
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119 Search PubMed Central for free full text articles containing the query stem cells:
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120
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121 +----------------------+--------------------------------------+
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122 | Parameter | Value |
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123 +======================+======================================+
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124 | NCBI Database to Use | PubMedCentral |
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125 +----------------------+--------------------------------------+
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126 | Term | Stem Cells AND free fulltext[filter] |
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127 +----------------------+--------------------------------------+
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128
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129 Search in Nucleotide for all tRNAs:
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130
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131 +----------------------+--------------------------------------+
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132 | Parameter | Value |
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133 +======================+======================================+
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134 | NCBI Database to Use | Nucleotide |
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135 +----------------------+--------------------------------------+
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136 | Term | biomol trna[prop] |
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137 +----------------------+--------------------------------------+
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138
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139 Search in Protein for a molecular weight range:
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140
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141 +----------------------+--------------------------------------+
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142 | Parameter | Value |
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143 +======================+======================================+
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144 | NCBI Database to Use | Protein |
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145 +----------------------+--------------------------------------+
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146 | Term | 70000:90000[molecular weight] |
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147 +----------------------+--------------------------------------+
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148
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149
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150 @REFERENCES@
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151
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152 @DISCLAIMER@
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153 ]]></help>
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154 <expand macro="citations"/>
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155 </tool>