Mercurial > repos > iuc > ncbi_eutils_efetch

comparison macros.xml @ 1:a42fa980bbd5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
author iuc
date Mon, 02 Nov 2015 12:59:23 -0500
parents 1b4ac594d02a
children cf56005c4320
comparison
equal deleted inserted replaced
0:1b4ac594d02a 1:a42fa980bbd5
4 <token name="@EMAIL_ARGUMENTS@"> 4 <token name="@EMAIL_ARGUMENTS@">
5 --user_email $__user_email__ 5 --user_email $__user_email__
6 #set admin_emails = ';'.join(str($__admin_users__).split(',')) 6 #set admin_emails = ';'.join(str($__admin_users__).split(','))
7 --admin_email $admin_emails 7 --admin_email $admin_emails
8 </token> 8 </token>
9 <!-- TODO: citation -->
9 <token name="@REFERENCES@"><![CDATA[ 10 <token name="@REFERENCES@"><![CDATA[
10 References 11 ]]></token>
11 ==========
12
13 If you use this Galaxy tool in work leading to a scientific
14 publication, please cite the following papers:
15
16 ]]></token>
17 <token name="@DISCLAIMER@"><![CDATA[ 12 <token name="@DISCLAIMER@"><![CDATA[
18 Usage Guidelines and Requirements 13 Usage Guidelines and Requirements
19 ================================= 14 =================================
20 15
21 Frequency, Timing, and Registration of E-utility URL Requests 16 Frequency, Timing, and Registration of E-utility URL Requests
88 external sites will abide by the same Privacy Policy to which NCBI 83 external sites will abide by the same Privacy Policy to which NCBI
89 adheres. It is the responsibility of the user to examine the copyright 84 adheres. It is the responsibility of the user to examine the copyright
90 and licensing restrictions of linked pages and to secure all necessary 85 and licensing restrictions of linked pages and to secure all necessary
91 permissions. 86 permissions.
92 ]]></token> 87 ]]></token>
93 <xml name="stdio"> 88 <xml name="dbselect"
94 <stdio> 89 token_name="db_select"
95 <!-- Anything other than zero is an error --> 90 token_label="NCBI Database to Use"
96 <exit_code range="1:"/> 91 >
97 <exit_code range=":-1"/> 92 <param name="@NAME@" type="select" label="@LABEL@">
98 <!-- In case the return code has not been set propery check stderr too -->
99 <regex match="Error:"/>
100 <regex match="Exception:"/>
101 </stdio>
102 </xml>
103 <xml name="dbselect">
104 <param name="db_select" type="select" label="NCBI Database to Use">
105 <option value="assembly">Assembly</option> 93 <option value="assembly">Assembly</option>
106 <option value="bioproject">BioProject</option> 94 <option value="bioproject">BioProject</option>
107 <option value="biosample">BioSample</option> 95 <option value="biosample">BioSample</option>
108 <option value="biosystems">Biosystems</option> 96 <option value="biosystems">Biosystems</option>
109 <option value="blastdbinfo">Blast Database Information</option> 97 <option value="blastdbinfo">Blast Database Information</option>
149 <option value="unigene">UniGene</option> 137 <option value="unigene">UniGene</option>
150 </param> 138 </param>
151 </xml> 139 </xml>
152 <xml name="db"> 140 <xml name="db">
153 <conditional name="db"> 141 <conditional name="db">
154 <param name="db_select" type="select" label="NCBI Database to Use"> 142 <expand macro="dbselect" />
155 <option value="assembly">Assembly</option>
156 <option value="bioproject">BioProject</option>
157 <option value="biosample">BioSample</option>
158 <option value="biosystems">Biosystems</option>
159 <option value="blastdbinfo">Blast Database Information</option>
160 <option value="books">Books</option>
161 <option value="cdd">Conserved Domains</option>
162 <option value="clinvar">Clinical Variants</option>
163 <option value="clone">CLone</option>
164 <option value="dbvar">dbVar</option>
165 <option value="epigenomics">Epigenomics</option>
166 <option value="gap">dbGaP</option>
167 <option value="gds">GEO Datasets</option>
168 <option value="gene">Gene</option>
169 <option value="genome">Genome</option>
170 <option value="geoprofiles">GEO Profiles</option>
171 <option value="gtr">Genetic Testing Registry</option>
172 <option value="homologene">HomoloGene</option>
173 <option value="journals">Journals</option>
174 <option value="medgen">MedGen</option>
175 <option value="mesh">MeSH</option>
176 <option value="ncbisearch">NCBI Web Site</option>
177 <option value="nlmcatalog">NLM Catalog</option>
178 <option value="nuccore">Nucleotide</option>
179 <option value="nucest">EST</option>
180 <option value="nucgss">GSS</option>
181 <option value="omim">OMIM</option>
182 <option value="pcassay">PubChem BioAssay</option>
183 <option value="pccompound">PubChem Compound</option>
184 <option value="pcsubstance">PubChem Substance</option>
185 <option value="pmc">PubMed Central</option>
186 <option value="popset">PopSet</option>
187 <option value="probe">Probe</option>
188 <option value="protein">Protein</option>
189 <option value="proteinclusters">Protein Clusters</option>
190 <option value="pubmed">PubMed</option>
191 <option value="pubmedhealth">PubMed Health</option>
192 <option value="snp">SNP</option>
193 <option value="sra">SRA</option>
194 <option value="structure">Structure</option>
195 <option value="taxonomy">Taxonomy</option>
196 <option value="toolkit">NCBI C++ Toolkit</option>
197 <option value="toolkitall">NCBI C++ Toolkit All</option>
198 <option value="toolkitbook">NCBI C++ Toolkit Book</option>
199 <option value="unigene">UniGene</option>
200 </param>
201 <when value="assembly"> 143 <when value="assembly">
202 <param name="output_format" type="select" label="Output Format"> 144 <param name="output_format" type="select" label="Output Format">
203 <option value="docsum-xml">Document summary</option> 145 <option value="docsum-xml">Document summary</option>
204 <option value="uilist-xml">List of UIDs (XML)</option> 146 <option value="uilist-xml">List of UIDs (XML)</option>
205 <option value="uilist-text">List of UIDs (plain text)</option> 147 <option value="uilist-text">List of UIDs (plain text)</option>
597 <option value="history">NCBI WebEnv History</option> 539 <option value="history">NCBI WebEnv History</option>
598 <option value="id_file">File containing IDs (one per line)</option> 540 <option value="id_file">File containing IDs (one per line)</option>
599 <option value="id_list">Direct Entry</option> 541 <option value="id_list">Direct Entry</option>
600 </param> 542 </param>
601 <when value="history"> 543 <when value="history">
602 <param label="History File" name="history_file" type="data" format="ncbi_history"/> 544 <param label="History File" name="history_file" type="data" format="json"/>
603 </when> 545 </when>
604 <when value="id_file"> 546 <when value="id_file">
605 <param label="ID List" name="id_file" type="data" format="text,tabular"/> 547 <param label="ID List" name="id_file" type="data" format="text,tabular"/>
606 </when> 548 </when>
607 <when value="id_list"> 549 <when value="id_list">
608 <param label="ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/> 550 <param label="ID List" name="id_list" type="text" area="true" help="Newline/Comma separated list of IDs"/>
609 </when> 551 </when>
610 </conditional> 552 </conditional>
611 </xml> 553 </xml>
612 <xml name="history_out"> 554 <xml name="history_out">
613 <data format="ncbi_history" name="history" label="NCBI Entrez WebEnv History"> 555 <data format="json" name="history" label="NCBI Entrez WebEnv History">
614 <yield/> 556 <yield/>
615 </data> 557 </data>
616 </xml> 558 </xml>
617 <xml name="citations"> 559 <xml name="citations">
618 <citations> 560 <citations>
623 publisher = {National Center for Biotechnology Information, Bethesda, Maryland}, 565 publisher = {National Center for Biotechnology Information, Bethesda, Maryland},
624 note = {http://ww.ncbi.nlm.nih.gov/books/NBK25500/} 566 note = {http://ww.ncbi.nlm.nih.gov/books/NBK25500/}
625 }</citation> 567 }</citation>
626 </citations> 568 </citations>
627 </xml> 569 </xml>
628 <xml name="db_select_to">
629 <param name="db_select_to" type="select" label="To NCBI Database">
630 <option value="assembly">Assembly</option>
631 <option value="bioproject">BioProject</option>
632 <option value="biosample">BioSample</option>
633 <option value="biosystems">Biosystems</option>
634 <option value="blastdbinfo">Blast Database Information</option>
635 <option value="books">Books</option>
636 <option value="cdd">Conserved Domains</option>
637 <option value="clinvar">Clinical Variants</option>
638 <option value="clone">CLone</option>
639 <option value="dbvar">dbVar</option>
640 <option value="epigenomics">Epigenomics</option>
641 <option value="gap">dbGaP</option>
642 <option value="gds">GEO Datasets</option>
643 <option value="gene">Gene</option>
644 <option value="genome">Genome</option>
645 <option value="geoprofiles">GEO Profiles</option>
646 <option value="gtr">Genetic Testing Registry</option>
647 <option value="homologene">HomoloGene</option>
648 <option value="journals">Journals</option>
649 <option value="medgen">MedGen</option>
650 <option value="mesh">MeSH</option>
651 <option value="ncbisearch">NCBI Web Site</option>
652 <option value="nlmcatalog">NLM Catalog</option>
653 <option value="nuccore">Nucleotide</option>
654 <option value="nucest">EST</option>
655 <option value="nucgss">GSS</option>
656 <option value="omim">OMIM</option>
657 <option value="pcassay">PubChem BioAssay</option>
658 <option value="pccompound">PubChem Compound</option>
659 <option value="pcsubstance">PubChem Substance</option>
660 <option value="pmc">PubMed Central</option>
661 <option value="popset">PopSet</option>
662 <option value="probe">Probe</option>
663 <option value="protein">Protein</option>
664 <option value="proteinclusters">Protein Clusters</option>
665 <option value="pubmed">PubMed</option>
666 <option value="pubmedhealth">PubMed Health</option>
667 <option value="snp">SNP</option>
668 <option value="sra">SRA</option>
669 <option value="structure">Structure</option>
670 <option value="taxonomy">Taxonomy</option>
671 <option value="toolkit">NCBI C++ Toolkit</option>
672 <option value="toolkitall">NCBI C++ Toolkit All</option>
673 <option value="toolkitbook">NCBI C++ Toolkit Book</option>
674 <option value="unigene">UniGene</option>
675 </param>
676 </xml>
677 <xml name="requirements"> 570 <xml name="requirements">
678 <requirements> 571 <requirements>
679 <requirement type="package" version="1.66">biopython</requirement> 572 <requirement type="package" version="1.66">biopython</requirement>
680 </requirements> 573 </requirements>
681 </xml> 574 </xml>