Mercurial > repos > iuc > ncbi_eutils_elink

annotate elink.xml @ 0:ffc6d6234c8a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
author iuc
date Sat, 31 Oct 2015 12:44:05 -0400
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children 127515819562
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0
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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1 <?xml version="1.0"?>
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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2 <tool id="ncbi_eutils_elink" name="NCBI ELink" version="@WRAPPER_VERSION@">
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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3 <description>link UIDs from one database to another</description>
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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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 <expand macro="stdio"/>
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9 <version_command>python elink.py --version</version_command>
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10 <command interpreter="python"><![CDATA[elink.py
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11 #if $cmd.cmd_select in ('neighbor', 'neighbor_score', 'neighbor_history'):
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12 $cmd.db_select_to
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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13 #else:
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14 "none"
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15 #end if
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16
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17 $db_select_from
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18 $cmd.cmd_select
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19
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20 @EMAIL_ARGUMENTS@
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21
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22 @LIST_OR_HIST@
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23
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24 #if $cmd.cmd_select == "neighbor_history":
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25 --history_out $history
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26 #end if
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27
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28 > $default]]></command>
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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29 <inputs>
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30 <param name="db_select_from" type="select" label="From NCBI Database">
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31 <option value="assembly">Assembly</option>
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32 <option value="bioproject">BioProject</option>
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33 <option value="biosample">BioSample</option>
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34 <option value="biosystems">Biosystems</option>
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35 <option value="blastdbinfo">Blast Database Information</option>
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36 <option value="books">Books</option>
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37 <option value="cdd">Conserved Domains</option>
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38 <option value="clinvar">Clinical Variants</option>
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39 <option value="clone">CLone</option>
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40 <option value="dbvar">dbVar</option>
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41 <option value="epigenomics">Epigenomics</option>
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42 <option value="gap">dbGaP</option>
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43 <option value="gds">GEO Datasets</option>
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44 <option value="gene">Gene</option>
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45 <option value="genome">Genome</option>
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46 <option value="geoprofiles">GEO Profiles</option>
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47 <option value="gtr">Genetic Testing Registry</option>
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48 <option value="homologene">HomoloGene</option>
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49 <option value="journals">Journals</option>
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50 <option value="medgen">MedGen</option>
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51 <option value="mesh">MeSH</option>
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52 <option value="ncbisearch">NCBI Web Site</option>
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53 <option value="nlmcatalog">NLM Catalog</option>
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54 <option value="nuccore">Nucleotide</option>
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55 <option value="nucest">EST</option>
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56 <option value="nucgss">GSS</option>
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57 <option value="omim">OMIM</option>
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58 <option value="pcassay">PubChem BioAssay</option>
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59 <option value="pccompound">PubChem Compound</option>
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60 <option value="pcsubstance">PubChem Substance</option>
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61 <option value="pmc">PubMed Central</option>
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62 <option value="popset">PopSet</option>
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63 <option value="probe">Probe</option>
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64 <option value="protein">Protein</option>
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65 <option value="proteinclusters">Protein Clusters</option>
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66 <option value="pubmed">PubMed</option>
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67 <option value="pubmedhealth">PubMed Health</option>
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68 <option value="snp">SNP</option>
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69 <option value="sra">SRA</option>
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70 <option value="structure">Structure</option>
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71 <option value="taxonomy">Taxonomy</option>
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72 <option value="toolkit">NCBI C++ Toolkit</option>
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73 <option value="toolkitall">NCBI C++ Toolkit All</option>
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74 <option value="toolkitbook">NCBI C++ Toolkit Book</option>
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75 <option value="unigene">UniGene</option>
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76 </param>
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77 <conditional name="cmd">
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78 <param name="cmd_select" type="select" label="ELink command to execute">
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79 <option value="neighbor">Neighbor: Fetch a set of UIDs in DB linked to input UIDs in DBFROM</option>
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80 <option value="neighbor_score">Scored Neighbors: Fetch a set of UIDs within the same database as the input UIDs along with computed similarity scores</option>
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81 <option value="neighbor_history">Neighbor (history): Fetch a set of UIDs in DB linked to input UIDs from DBFROM, and store on history server</option>
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82 <option value="acheck">ACheck: List all links available from a set of UIDs</option>
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83 <option value="ncheck">NCheck: Check for the existence of links within the same database for a set of UIDs</option>
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84 <option value="lcheck">LCheck: Check for the existence of external links (LinkOuts) for a set of UIDs</option>
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85 <option value="llinks">Links: For each input UID, list the URLs and attributes for the LinkOut providers that are not libraries</option>
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86 <option value="llinkslib">LinksLib: For each input UID, list the URLs and attributes for the LinkOut providers (including libraries)</option>
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87 <option value="prlinks">Provider Links: List the primary LinkOut provider for each input UID</option>
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88 </param>
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89 <when value="neighbor">
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90 <expand macro="db_select_to"/>
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91 </when>
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92 <when value="neighbor_score">
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93 <expand macro="db_select_to"/>
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94 </when>
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95 <when value="neighbor_history">
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96 <expand macro="db_select_to"/>
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97 </when>
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98 <when value="acheck">
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99 <expand macro="db_select_to"/>
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100 </when>
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101 <when value="ncheck"/>
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102 <when value="lcheck"/>
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103 <when value="llinks"/>
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104 <when value="llinkslib"/>
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105 <when value="prlinks"/>
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106 </conditional>
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107 <expand macro="list_or_hist"/>
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108 </inputs>
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109 <outputs>
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110 <data format="xml" name="default" label="NCBI Linked IDs from $db_select_from"/>
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111 <expand macro="history_out">
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112 <filter>cmd['cmd_select'] == 'neighbor_history'</filter>
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113 </expand>
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114 </outputs>
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115 <tests>
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116 <test>
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117 <param name="cmd_select" value="neighbor"/>
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118 <param name="db_select_to" value="pubmed"/>
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119 <param name="db_select_from" value="taxonomy"/>
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120 <param name="qss" value="id_list"/>
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121 <param name="id_list" value="510899"/>
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122 <output name="default" file="pm-tax-neighbor.xml"/>
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123 </test>
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124 </tests>
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125 <help><![CDATA[
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126 NCBI Entrez ELink
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127 =================
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128
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129 Responds to a list of UIDs in a given database with either a list of related
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130 UIDs (and relevancy scores) in the same database or a list of linked UIDs in
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131 another Entrez database; checks for the existence of a specified link from a
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132 list of one or more UIDs; creates a hyperlink to the primary LinkOut provider
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133 for a specific UID and database, or lists LinkOut URLs and attributes for
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134 multiple UIDs.
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135
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136 Commands
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137 --------
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138
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139 Example Queries
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140 ---------------
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141
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142 Link from protein to gene
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143
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144 +----------------------+--------------------------------------+
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145 | Parameter | Value |
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146 +======================+======================================+
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147 | From NCBI Database | Protein |
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148 +----------------------+--------------------------------------+
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149 | Elink Command | Neighbor |
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150 +----------------------+--------------------------------------+
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151 | To NCBI Database | Gene |
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152 +----------------------+--------------------------------------+
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153 | ID List | 15718680 157427902 |
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154 +----------------------+--------------------------------------+
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155
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156 Find related articles to PMID 20210808 with scores
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157
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158 +----------------------+--------------------------------------+
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159 | Parameter | Value |
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160 +======================+======================================+
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161 | From NCBI Database | PubMed |
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162 +----------------------+--------------------------------------+
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163 | Elink Command | Scored Neighbors |
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164 +----------------------+--------------------------------------+
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165 | To NCBI Database | PubMed |
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166 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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167 | ID List | 20210808 |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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168 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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169
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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170 List all possible links from two protein GIs
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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171
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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172 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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173 | Parameter | Value |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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174 +======================+======================================+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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175 | From NCBI Database | Protein |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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176 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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177 | Elink Command | ACheck |
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178 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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179 | ID List | 15718680 157427902 |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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180 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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181
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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182 List all possible links from two protein GIs to PubMed
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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183
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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184 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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185 | Parameter | Value |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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186 +======================+======================================+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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187 | From NCBI Database | Protein |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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188 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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189 | Elink Command | ACheck |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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190 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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191 | To NCBI Database | PubMed |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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192 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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193 | ID List | 15718680 157427902 |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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194 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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195
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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196 Check whether two nuccore sequences have "related sequences" links.
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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197
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198 +----------------------+--------------------------------------+
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199 | Parameter | Value |
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200 +======================+======================================+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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201 | From NCBI Database | Nuccore |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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202 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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203 | Elink Command | NCheck |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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204 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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205 | ID List | 21614549 219152114 |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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206 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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207
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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208 List the LinkOut URLs for non-library providers for two pubmed abstracts.
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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209
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210 +----------------------+--------------------------------------+
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211 | Parameter | Value |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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212 +======================+======================================+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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213 | From NCBI Database | Pubmed |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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214 +----------------------+--------------------------------------+
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215 | Elink Command | Links |
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216 +----------------------+--------------------------------------+
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217 | ID List | 19880848 19822630 |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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218 +----------------------+--------------------------------------+
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219
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220 Find links to full text providers for two PubMed abstracts.
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221
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222 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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223 | Parameter | Value |
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224 +======================+======================================+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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225 | From NCBI Database | Pubmed |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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226 +----------------------+--------------------------------------+
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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227 | Elink Command | Provider Links |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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228 +----------------------+--------------------------------------+
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229 | ID List | 19880848 19822630 |
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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230 +----------------------+--------------------------------------+
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231
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232 @REFERENCES@
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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233
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234 @DISCLAIMER@
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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235 ]]></help>
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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236 <expand macro="citations"/>
ffc6d6234c8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 780c9984a9c44d046aadf1e316a668d1e53aa1f0
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237 </tool>