Mercurial > repos > iuc > ncbi_eutils_elink

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 851b88d92fa7740880a5edf407f629bf3f7f7bf0
author iuc
date Fri, 04 Oct 2024 14:35:37 +0000
parents e4f8623b8b9b
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1ed9a99b9b1f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit db33413a06c275efd4cc8e771c37facf543a2cfa"
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1 <tool id="ncbi_eutils_elink" name="NCBI ELink" version="@WRAPPER_VERSION@" profile="@PROFILE@">
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2 <description>link UIDs from one database to another</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>python elink.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 python '$__tool_directory__/elink.py'
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10
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11 @LINK_TOKEN@
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13 @EMAIL_ARGUMENTS@
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15 @LIST_OR_HIST@
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17 > $default]]></command>
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18 <inputs>
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19 <expand macro="list_or_hist"/>
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20 <expand macro="linkmacro"/>
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21 </inputs>
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22 <outputs>
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23 <data format="xml" name="default" label="NCBI ${cmd.cmd_select} Links From ${cmd.db_from_link.db_select_from_link} To ${cmd.db_from_link.db_to.db_select_to} Via ${cmd.db_from_link.db_to.linkname}">
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24 <change_format>
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25 <when input="cmd.output_format" value="xml" format="xml" />
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26 <when input="cmd.output_format" value="json" format="json" />
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27 <when input="cmd.output_format" value="text" format="tabular" />
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28 </change_format>
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29 <filter>query_source['qss'] != 'history_json' and query_source['qss'] != 'history_xml'</filter>
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30 </data>
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31 <collection name="linksets" type="list" label="NCBI ${cmd.cmd_select} Links From ${cmd.db_from_link.db_select_from_link} To ${cmd.db_from_link.db_to.db_select_to} Via All">
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32 <discover_datasets pattern="__designation_and_ext__" directory="downloads"/>
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33 <filter>query_source['qss'] == 'history_json' or query_source['qss'] == 'history_xml'</filter>
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34 </collection>
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35 </outputs>
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36 <tests>
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37 <test expect_num_outputs="1">
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38 <param name="cmd_select" value="neighbor"/>
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39 <param name="db_select_to" value="pubmed"/>
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40 <param name="db_select_from_link" value="taxonomy"/>
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41 <param name="qss" value="id_list"/>
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42 <param name="id_list" value="510899"/>
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43 <param name="output_format" value="xml"/>
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44 <param name="linkname" value="None"/>
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45 <output name="default" file="pm-tax-neighbor.xml" ftype="xml"/>
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46 </test>
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47 <test expect_num_outputs="1">
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48 <param name="cmd_select" value="neighbor"/>
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49 <param name="db_select_to" value="nuccore"/>
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50 <param name="db_select_from_link" value="gene"/>
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51 <param name="qss" value="id_xml"/>
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52 <param name="id_xml" value="elink.esearch_in_xmlid.xml"/>
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53 <param name="output_format" value="text"/>
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54 <param name="linkname" value="gene_nuccore"/>
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55 <output name="default" ftype="tabular">
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56 <assert_contents>
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57 <has_line line="1899688395"/>
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58 <has_line line="1896832511"/>
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59 </assert_contents>
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60 </output>
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61 </test>
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62 <test expect_num_outputs="1">
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63 <param name="cmd_select" value="neighbor"/>
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64 <param name="db_select_to" value="nuccore"/>
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65 <param name="db_select_from_link" value="gene"/>
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66 <param name="qss" value="id_json"/>
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67 <param name="id_json" value="elink.esearchin_id.json"/>
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68 <param name="output_format" value="json"/>
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69 <param name="linkname" value="None"/>
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70 <output name="default" ftype="json">
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71 <assert_contents>
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72 <has_text text="gene_nuccore_refseqrna"/>
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73 <has_text text="gene_nuccore"/>
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74 <has_text text="1899688395"/>
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75 </assert_contents>
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76 </output>
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77 </test>
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78 <test expect_num_outputs="1">
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79 <param name="cmd_select" value="neighbor"/>
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80 <param name="db_select_to" value="nuccore"/>
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81 <param name="db_select_from_link" value="gene"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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82 <param name="qss" value="id_file"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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83 <param name="id_file" value="elink.esearchin_id.tabular"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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84 <param name="output_format" value="xml"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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85 <param name="linkname" value="gene_nuccore_refseqrna"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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86 <output name="default" file="elink.esearchin_id_1link.xml" ftype="xml"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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87 </test>
5
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88 <test expect_num_outputs="1">
3
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89 <param name="cmd_select" value="neighbor_history"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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90 <param name="db_select_to" value="gene"/>
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91 <param name="db_select_from_link" value="nuccore"/>
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92 <param name="qss" value="id_json"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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93 <param name="id_json" value="elink.elinkin_1link.json"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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94 <param name="output_format" value="json"/>
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95 <param name="linkname" value="nuccore_gene"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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96 <output name="default" file="elink.elinkin_1link_hist.json" ftype="json" lines_diff="2"/>
55b3067762f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit dae34e5e182b4cceb808d7353080f14aa9a78ca9"
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97 </test>
5
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98 <test expect_num_outputs="1">
3
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99 <param name="cmd_select" value="neighbor_history"/>
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100 <param name="db_select_to" value="gene"/>
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101 <param name="db_select_from_link" value="nuccore"/>
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102 <param name="qss" value="id_xml"/>
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103 <param name="id_xml" value="elink.elinkin_alllinks_id.xml"/>
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104 <param name="output_format" value="xml"/>
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105 <param name="linkname" value="nuccore_gene"/>
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106 <output name="default" file="elink.elinkin_allalllinks_id.xml" ftype="xml" lines_diff="2"/>
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107 </test>
5
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108 <test expect_num_outputs="1">
3
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109 <param name="cmd_select" value="neighbor_score"/>
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110 <param name="db_select_to" value="gene"/>
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111 <param name="db_select_from_link" value="nuccore"/>
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112 <param name="qss" value="id_list"/>
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113 <param name="id_list" value="1899688395"/>
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114 <param name="output_format" value="text"/>
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115 <param name="linkname" value="nuccore_gene"/>
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116 <output name="default" file="elink.elinkin_1link_id.tabular" ftype="tabular"/>
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117 </test>
0
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118 </tests>
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119 <help><![CDATA[
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120 NCBI Entrez ELink
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121 =================
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122
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123 Responds to a list of UIDs in a given database with either a list of related
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124 UIDs (and relevancy scores) in the same database or a list of linked UIDs in
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125 another Entrez database; checks for the existence of a specified link from a
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126 list of one or more UIDs; creates a hyperlink to the primary LinkOut provider
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127 for a specific UID and database, or lists LinkOut URLs and attributes for
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128 multiple UIDs.
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129
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130 Commands
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131 --------
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132
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133 Example Queries
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134 ---------------
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135
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136 Link from protein to gene
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137
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138 +----------------------+--------------------------------------+
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139 | Parameter | Value |
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140 +======================+======================================+
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141 | From NCBI Database | Protein |
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142 +----------------------+--------------------------------------+
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143 | Elink Command | Neighbor |
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144 +----------------------+--------------------------------------+
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145 | To NCBI Database | Gene |
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146 +----------------------+--------------------------------------+
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147 | ID List | 15718680 157427902 |
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148 +----------------------+--------------------------------------+
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149
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150 Find related articles to PMID 20210808 with scores
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151
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152 +----------------------+--------------------------------------+
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153 | Parameter | Value |
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154 +======================+======================================+
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155 | From NCBI Database | PubMed |
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156 +----------------------+--------------------------------------+
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157 | Elink Command | Scored Neighbors |
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158 +----------------------+--------------------------------------+
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159 | To NCBI Database | PubMed |
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160 +----------------------+--------------------------------------+
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161 | ID List | 20210808 |
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162 +----------------------+--------------------------------------+
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163
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164 List all possible links from two protein GIs
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165
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166 +----------------------+--------------------------------------+
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167 | Parameter | Value |
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168 +======================+======================================+
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169 | From NCBI Database | Protein |
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170 +----------------------+--------------------------------------+
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171 | Elink Command | ACheck |
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172 +----------------------+--------------------------------------+
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173 | ID List | 15718680 157427902 |
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174 +----------------------+--------------------------------------+
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175
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176 List all possible links from two protein GIs to PubMed
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177
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178 +----------------------+--------------------------------------+
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179 | Parameter | Value |
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180 +======================+======================================+
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181 | From NCBI Database | Protein |
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182 +----------------------+--------------------------------------+
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183 | Elink Command | ACheck |
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184 +----------------------+--------------------------------------+
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185 | To NCBI Database | PubMed |
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186 +----------------------+--------------------------------------+
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187 | ID List | 15718680 157427902 |
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188 +----------------------+--------------------------------------+
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189
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190 Check whether two nuccore sequences have "related sequences" links.
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191
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192 +----------------------+--------------------------------------+
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193 | Parameter | Value |
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194 +======================+======================================+
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195 | From NCBI Database | Nuccore |
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196 +----------------------+--------------------------------------+
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197 | Elink Command | NCheck |
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198 +----------------------+--------------------------------------+
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199 | ID List | 21614549 219152114 |
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200 +----------------------+--------------------------------------+
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201
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202 List the LinkOut URLs for non-library providers for two pubmed abstracts.
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203
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204 +----------------------+--------------------------------------+
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205 | Parameter | Value |
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206 +======================+======================================+
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207 | From NCBI Database | Pubmed |
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208 +----------------------+--------------------------------------+
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209 | Elink Command | Links |
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210 +----------------------+--------------------------------------+
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211 | ID List | 19880848 19822630 |
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212 +----------------------+--------------------------------------+
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213
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214 Find links to full text providers for two PubMed abstracts.
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215
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216 +----------------------+--------------------------------------+
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217 | Parameter | Value |
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218 +======================+======================================+
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219 | From NCBI Database | Pubmed |
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220 +----------------------+--------------------------------------+
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221 | Elink Command | Provider Links |
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222 +----------------------+--------------------------------------+
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223 | ID List | 19880848 19822630 |
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224 +----------------------+--------------------------------------+
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225
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226 @REFERENCES@
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227
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228 @DISCLAIMER@
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229 ]]></help>
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230 <expand macro="citations"/>
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231 </tool>