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changeset 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
files README.md README.rst efetch.xml macros.xml requirements.txt test-data/egquery.1.xml test-data/pubmed.metadata.xml tool_dependencies.xml
diffstat 8 files changed, 50 insertions(+), 1144 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Sat Oct 31 12:44:54 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-# Galaxy NCBI Entrez Tools
-
-This repo requires a readme as administrators should very aware of some
-restrictions NCBI places on the use of the Entrez service.
-
-NCBI requests that you please limit large jobs to either weekends or between
-9:00 PM and 5:00 AM Eastern time during weekdays. This is not a request that
-the Galaxy tool can easily service, so we've included it in the disclaimer on
-every tool quite prominently.
-
-Failure to comply with NCBI's policies may result in an block until you/the
-user contacts NCBI and registers the tool ID and their email.
-
-Note that these are *IP* level blocks so the Galaxy tools uses a concatenation
-of the administrator's emails, and the user email, in hopes that NCBI will
-contact all relevant parties should their system be abused.
-
-Additionally, since these are IP level blocks, the Galaxy tool author (@erasche) recommends
-using the following `jobs_conf.xml` snippet in order to place a system-wide
-restriction of 1 concurrent Entrez job amongst all users.
-
-```xml
-<destination id="entrez" runner="local">
-</destination>
-<limit type="concurrent_jobs" id="entrez">1</limit>
-<tools>
-  <tool id="ncbi.eutils.efetch" destination="entrez" />
-  <tool id="ncbi.eutils.esearch" destination="entrez" />
-  <tool id="ncbi.eutils.epost" destination="entrez" />
-  <tool id="ncbi.eutils.elink" destination="entrez" />
-  <tool id="ncbi.eutils.einfo" destination="entrez" />
-  <tool id="ncbi.eutils.esummary" destination="entrez" />
-</tools>
-```
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Nov 02 12:59:23 2015 -0500
@@ -0,0 +1,38 @@
+Galaxy NCBI Entrez Tools
+========================
+
+This repo requires a readme as administrators should very aware of some
+restrictions NCBI places on the use of the Entrez service.
+
+NCBI requests that you please limit large jobs to either weekends or
+between 9:00 PM and 5:00 AM Eastern time during weekdays. This is not a
+request that the Galaxy tool can easily service, so we've included it in
+the disclaimer on every tool quite prominently.
+
+Failure to comply with NCBI's policies may result in an block until
+you/the user contacts NCBI and registers the tool ID and their email.
+
+Note that these are *IP* level blocks so the Galaxy tools uses a
+concatenation of the administrator's emails, and the user email, in
+hopes that NCBI will contact all relevant parties should their system be
+abused.
+
+Additionally, since these are IP level blocks, the Galaxy tool author
+(@erasche) recommends using the following ``jobs_conf.xml`` snippet in
+order to place a system-wide restriction of 1 concurrent Entrez job
+amongst all users.
+
+.. code:: xml
+
+    <destination id="entrez" runner="local">
+    </destination>
+    <limit type="concurrent_jobs" id="entrez">1</limit>
+    <tools>
+      <tool id="ncbi.eutils.efetch" destination="entrez" />
+      <tool id="ncbi.eutils.esearch" destination="entrez" />
+      <tool id="ncbi.eutils.epost" destination="entrez" />
+      <tool id="ncbi.eutils.elink" destination="entrez" />
+      <tool id="ncbi.eutils.einfo" destination="entrez" />
+      <tool id="ncbi.eutils.esummary" destination="entrez" />
+    </tools>
+
--- a/efetch.xml	Sat Oct 31 12:44:54 2015 -0400
+++ b/efetch.xml	Mon Nov 02 12:59:23 2015 -0500
@@ -5,9 +5,8 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python efetch.py --version</version_command>
-  <command interpreter="python"><![CDATA[efetch.py
+  <command detect_errors="aggressive" interpreter="python"><![CDATA[efetch.py
 $db.db_select
 
 @LIST_OR_HIST@
@@ -77,7 +76,6 @@
       <param name="qss" value="id_list"/>
       <param name="id_list" value="10239"/>
       <output name="default" file="viruses.tax.xml">
-        <!--<discovered_datasets designation="0" ftytpe="xml" file="viruses.tax.xml" />-->
       </output>
     </test>
   </tests>
--- a/macros.xml	Sat Oct 31 12:44:54 2015 -0400
+++ b/macros.xml	Mon Nov 02 12:59:23 2015 -0500
@@ -6,14 +6,9 @@
 #set admin_emails = ';'.join(str($__admin_users__).split(','))
 --admin_email $admin_emails
   </token>
+  <!--  TODO: citation -->
   <token name="@REFERENCES@"><![CDATA[
-References
-==========
-
-If you use this Galaxy tool in work leading to a scientific
-publication, please cite the following papers:
-
-        ]]></token>
+  ]]></token>
   <token name="@DISCLAIMER@"><![CDATA[
 Usage Guidelines and Requirements
 =================================
@@ -90,18 +85,11 @@
 and licensing restrictions of linked pages and to secure all necessary
 permissions.
         ]]></token>
-  <xml name="stdio">
-    <stdio>
-      <!-- Anything other than zero is an error -->
-      <exit_code range="1:"/>
-      <exit_code range=":-1"/>
-      <!-- In case the return code has not been set propery check stderr too -->
-      <regex match="Error:"/>
-      <regex match="Exception:"/>
-    </stdio>
-  </xml>
-  <xml name="dbselect">
-    <param name="db_select" type="select" label="NCBI Database to Use">
+    <xml name="dbselect"
+        token_name="db_select"
+        token_label="NCBI Database to Use"
+        >
+    <param name="@NAME@" type="select" label="@LABEL@">
       <option value="assembly">Assembly</option>
       <option value="bioproject">BioProject</option>
       <option value="biosample">BioSample</option>
@@ -151,53 +139,7 @@
   </xml>
   <xml name="db">
     <conditional name="db">
-      <param name="db_select" type="select" label="NCBI Database to Use">
-        <option value="assembly">Assembly</option>
-        <option value="bioproject">BioProject</option>
-        <option value="biosample">BioSample</option>
-        <option value="biosystems">Biosystems</option>
-        <option value="blastdbinfo">Blast Database Information</option>
-        <option value="books">Books</option>
-        <option value="cdd">Conserved Domains</option>
-        <option value="clinvar">Clinical Variants</option>
-        <option value="clone">CLone</option>
-        <option value="dbvar">dbVar</option>
-        <option value="epigenomics">Epigenomics</option>
-        <option value="gap">dbGaP</option>
-        <option value="gds">GEO Datasets</option>
-        <option value="gene">Gene</option>
-        <option value="genome">Genome</option>
-        <option value="geoprofiles">GEO Profiles</option>
-        <option value="gtr">Genetic Testing Registry</option>
-        <option value="homologene">HomoloGene</option>
-        <option value="journals">Journals</option>
-        <option value="medgen">MedGen</option>
-        <option value="mesh">MeSH</option>
-        <option value="ncbisearch">NCBI Web Site</option>
-        <option value="nlmcatalog">NLM Catalog</option>
-        <option value="nuccore">Nucleotide</option>
-        <option value="nucest">EST</option>
-        <option value="nucgss">GSS</option>
-        <option value="omim">OMIM</option>
-        <option value="pcassay">PubChem BioAssay</option>
-        <option value="pccompound">PubChem Compound</option>
-        <option value="pcsubstance">PubChem Substance</option>
-        <option value="pmc">PubMed Central</option>
-        <option value="popset">PopSet</option>
-        <option value="probe">Probe</option>
-        <option value="protein">Protein</option>
-        <option value="proteinclusters">Protein Clusters</option>
-        <option value="pubmed">PubMed</option>
-        <option value="pubmedhealth">PubMed Health</option>
-        <option value="snp">SNP</option>
-        <option value="sra">SRA</option>
-        <option value="structure">Structure</option>
-        <option value="taxonomy">Taxonomy</option>
-        <option value="toolkit">NCBI C++ Toolkit</option>
-        <option value="toolkitall">NCBI C++ Toolkit All</option>
-        <option value="toolkitbook">NCBI C++ Toolkit Book</option>
-        <option value="unigene">UniGene</option>
-      </param>
+      <expand macro="dbselect" />
       <when value="assembly">
         <param name="output_format" type="select" label="Output Format">
           <option value="docsum-xml">Document summary</option>
@@ -599,7 +541,7 @@
         <option value="id_list">Direct Entry</option>
       </param>
       <when value="history">
-        <param label="History File" name="history_file" type="data" format="ncbi_history"/>
+        <param label="History File" name="history_file" type="data" format="json"/>
       </when>
       <when value="id_file">
         <param label="ID List" name="id_file" type="data" format="text,tabular"/>
@@ -610,7 +552,7 @@
     </conditional>
   </xml>
   <xml name="history_out">
-    <data format="ncbi_history" name="history" label="NCBI Entrez WebEnv History">
+    <data format="json" name="history" label="NCBI Entrez WebEnv History">
       <yield/>
     </data>
   </xml>
@@ -625,55 +567,6 @@
       }</citation>
     </citations>
   </xml>
-  <xml name="db_select_to">
-    <param name="db_select_to" type="select" label="To NCBI Database">
-      <option value="assembly">Assembly</option>
-      <option value="bioproject">BioProject</option>
-      <option value="biosample">BioSample</option>
-      <option value="biosystems">Biosystems</option>
-      <option value="blastdbinfo">Blast Database Information</option>
-      <option value="books">Books</option>
-      <option value="cdd">Conserved Domains</option>
-      <option value="clinvar">Clinical Variants</option>
-      <option value="clone">CLone</option>
-      <option value="dbvar">dbVar</option>
-      <option value="epigenomics">Epigenomics</option>
-      <option value="gap">dbGaP</option>
-      <option value="gds">GEO Datasets</option>
-      <option value="gene">Gene</option>
-      <option value="genome">Genome</option>
-      <option value="geoprofiles">GEO Profiles</option>
-      <option value="gtr">Genetic Testing Registry</option>
-      <option value="homologene">HomoloGene</option>
-      <option value="journals">Journals</option>
-      <option value="medgen">MedGen</option>
-      <option value="mesh">MeSH</option>
-      <option value="ncbisearch">NCBI Web Site</option>
-      <option value="nlmcatalog">NLM Catalog</option>
-      <option value="nuccore">Nucleotide</option>
-      <option value="nucest">EST</option>
-      <option value="nucgss">GSS</option>
-      <option value="omim">OMIM</option>
-      <option value="pcassay">PubChem BioAssay</option>
-      <option value="pccompound">PubChem Compound</option>
-      <option value="pcsubstance">PubChem Substance</option>
-      <option value="pmc">PubMed Central</option>
-      <option value="popset">PopSet</option>
-      <option value="probe">Probe</option>
-      <option value="protein">Protein</option>
-      <option value="proteinclusters">Protein Clusters</option>
-      <option value="pubmed">PubMed</option>
-      <option value="pubmedhealth">PubMed Health</option>
-      <option value="snp">SNP</option>
-      <option value="sra">SRA</option>
-      <option value="structure">Structure</option>
-      <option value="taxonomy">Taxonomy</option>
-      <option value="toolkit">NCBI C++ Toolkit</option>
-      <option value="toolkitall">NCBI C++ Toolkit All</option>
-      <option value="toolkitbook">NCBI C++ Toolkit Book</option>
-      <option value="unigene">UniGene</option>
-    </param>
-  </xml>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="1.66">biopython</requirement>
--- a/requirements.txt	Sat Oct 31 12:44:54 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-biopython
--- a/test-data/egquery.1.xml	Sat Oct 31 12:44:54 2015 -0400
+++ b/test-data/egquery.1.xml	Mon Nov 02 12:59:23 2015 -0500
@@ -5,46 +5,3 @@
     <Term>bacteriophage</Term>
     
     <eGQueryResult>
-        <ResultItem><DbName>pubmed</DbName><MenuName>PubMed</MenuName><Count>62489</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>pmc</DbName><MenuName>PubMed Central</MenuName><Count>90071</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>mesh</DbName><MenuName>MeSH</MenuName><Count>271</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>books</DbName><MenuName>Books</MenuName><Count>786</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>pubmedhealth</DbName><MenuName>PubMed Health</MenuName><Count>7</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>omim</DbName><MenuName>OMIM</MenuName><Count>17</Count><Status>Ok</Status></ResultItem>
-        
-        <ResultItem><DbName>ncbisearch</DbName><MenuName>Site Search</MenuName><Count>27</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>nuccore</DbName><MenuName>Nucleotide</MenuName><Count>446855</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>nucgss</DbName><MenuName>GSS</MenuName><Count>723</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>nucest</DbName><MenuName>EST</MenuName><Count>1018</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>protein</DbName><MenuName>Protein</MenuName><Count>655232</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>genome</DbName><MenuName>Genome</MenuName><Count>15</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>structure</DbName><MenuName>Structure</MenuName><Count>3145</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>taxonomy</DbName><MenuName>Taxonomy</MenuName><Count>1</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>snp</DbName><MenuName>SNP</MenuName><Count>0</Count><Status>Term or Database is not found</Status></ResultItem>
-        <ResultItem><DbName>dbvar</DbName><MenuName>dbVar</MenuName><Count>0</Count><Status>Term or Database is not found</Status></ResultItem>
-        <ResultItem><DbName>epigenomics</DbName><MenuName>Epigenomics</MenuName><Count>1</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>gene</DbName><MenuName>Gene</MenuName><Count>51399</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>sra</DbName><MenuName>SRA</MenuName><Count>209</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>biosystems</DbName><MenuName>BioSystems</MenuName><Count>255</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>unigene</DbName><MenuName>UniGene</MenuName><Count>7</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>cdd</DbName><MenuName>Conserved Domains</MenuName><Count>321</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>clone</DbName><MenuName>Clone</MenuName><Count>0</Count><Status>Term or Database is not found</Status></ResultItem>
-        
-        <ResultItem><DbName>popset</DbName><MenuName>PopSet</MenuName><Count>159</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>geoprofiles</DbName><MenuName>GEO Profiles</MenuName><Count>1083</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>gds</DbName><MenuName>GEO DataSets</MenuName><Count>1289</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>homologene</DbName><MenuName>HomoloGene</MenuName><Count>21</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>pccompound</DbName><MenuName>PubChem Compound</MenuName><Count>4</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>pcsubstance</DbName><MenuName>PubChem Substance</MenuName><Count>586</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>pcassay</DbName><MenuName>PubChem BioAssay</MenuName><Count>287</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>nlmcatalog</DbName><MenuName>NLM Catalog</MenuName><Count>450</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>probe</DbName><MenuName>Probe</MenuName><Count>641</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>gap</DbName><MenuName>dbGaP</MenuName><Count>0</Count><Status>Term or Database is not found</Status></ResultItem>
-        <ResultItem><DbName>proteinclusters</DbName><MenuName>Protein Clusters</MenuName><Count>714</Count><Status>Ok</Status></ResultItem>
-        
-        <ResultItem><DbName>bioproject</DbName><MenuName>BioProject</MenuName><Count>127</Count><Status>Ok</Status></ResultItem>
-        <ResultItem><DbName>biosample</DbName><MenuName>BioSample</MenuName><Count>150</Count><Status>Ok</Status></ResultItem>
-    </eGQueryResult>
-    
-</Result>
-
--- a/test-data/pubmed.metadata.xml	Sat Oct 31 12:44:54 2015 -0400
+++ b/test-data/pubmed.metadata.xml	Mon Nov 02 12:59:23 2015 -0500
@@ -5,948 +5,3 @@
 	<DbName>pubmed</DbName>
 	<MenuName>PubMed</MenuName>
 	<Description>PubMed bibliographic record</Description>
-	<DbBuild>Build150413-2207m.6</DbBuild>
-	<Count>24802558</Count>
-	<LastUpdate>2015/04/14 12:42</LastUpdate>
-	<FieldList>
-		<Field>
-			<Name>ALL</Name>
-			<FullName>All Fields</FullName>
-			<Description>All terms from all searchable fields</Description>
-			<TermCount>154691781</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>N</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>UID</Name>
-			<FullName>UID</FullName>
-			<Description>Unique number assigned to publication</Description>
-			<TermCount>0</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>Y</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>Y</IsHidden>
-		</Field>
-		<Field>
-			<Name>FILT</Name>
-			<FullName>Filter</FullName>
-			<Description>Limits the records</Description>
-			<TermCount>8601</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>TITL</Name>
-			<FullName>Title</FullName>
-			<Description>Words in title of publication</Description>
-			<TermCount>15268356</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>N</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>WORD</Name>
-			<FullName>Text Word</FullName>
-			<Description>Free text associated with publication</Description>
-			<TermCount>52358108</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>N</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>MESH</Name>
-			<FullName>MeSH Terms</FullName>
-			<Description>Medical Subject Headings assigned to publication</Description>
-			<TermCount>600878</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>Y</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>MAJR</Name>
-			<FullName>MeSH Major Topic</FullName>
-			<Description>MeSH terms of major importance to publication</Description>
-			<TermCount>536728</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>Y</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>AUTH</Name>
-			<FullName>Author</FullName>
-			<Description>Author(s) of publication</Description>
-			<TermCount>13401867</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>JOUR</Name>
-			<FullName>Journal</FullName>
-			<Description>Journal abbreviation of publication</Description>
-			<TermCount>171935</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>AFFL</Name>
-			<FullName>Affiliation</FullName>
-			<Description>Author&apos;s institutional affiliation and address</Description>
-			<TermCount>29621384</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>N</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>ECNO</Name>
-			<FullName>EC/RN Number</FullName>
-			<Description>EC number for enzyme or CAS registry number</Description>
-			<TermCount>93885</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>SUBS</Name>
-			<FullName>Supplementary Concept</FullName>
-			<Description>CAS chemical name or MEDLINE Substance Name</Description>
-			<TermCount>237211</TermCount>
-			<IsDate>N</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>PDAT</Name>
-			<FullName>Date - Publication</FullName>
-			<Description>Date of publication</Description>
-			<TermCount>37386</TermCount>
-			<IsDate>Y</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>EDAT</Name>
-			<FullName>Date - Entrez</FullName>
-			<Description>Date publication first accessible through Entrez</Description>
-			<TermCount>36028</TermCount>
-			<IsDate>Y</IsDate>
-			<IsNumerical>N</IsNumerical>
-			<SingleToken>Y</SingleToken>
-			<Hierarchy>N</Hierarchy>
-			<IsHidden>N</IsHidden>
-		</Field>
-		<Field>
-			<Name>VOL</Name>
-			<FullName>Volume</FullName>
-			<Description>Volume number of publication</Description>
-			<TermCount>13557</TermCount>
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-				<Menu>Nucleotide Links</Menu>
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-				<Menu>EST Links</Menu>
-				<Description>Expressed Sequence Tag (EST) nucleotide sequence records reported in the current articles.</Description>
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-			<Link>
-				<Name>pubmed_nucgss</Name>
-				<Menu>GSS Links</Menu>
-				<Description>Genome Survey Sequence (GSS) nucleotide records reported in the current articles.</Description>
-				<DbTo>nucgss</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_omim_bookrecords</Name>
-				<Menu>OMIM (from Bookshelf)</Menu>
-				<Description>OMIM records in this citation</Description>
-				<DbTo>omim</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_omim_calculated</Name>
-				<Menu>OMIM (calculated) Links</Menu>
-				<Description>Online Mendelian Inheritance in Man (OMIM) records that include the current articles as references in the light bulb links within or in the citations at the end of the OMIM record. The references available through the light bulb link are collected using the PubMed related articles algorithm to identify records with similar terminology to the OMIM record.</Description>
-				<DbTo>omim</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_omim_cited</Name>
-				<Menu>OMIM (cited) Links</Menu>
-				<Description>Online Mendelian Inheritance in Man (OMIM) records that include the current articles as reference cited at the end of the OMIM record.</Description>
-				<DbTo>omim</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pcassay</Name>
-				<Menu>PubChem BioAssay</Menu>
-				<Description>PubChem BioAssay experiments on the biological activities of small molecules that cite the current articles. The depositors of BioAssay data provide these references.</Description>
-				<DbTo>pcassay</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pccompound</Name>
-				<Menu>PubChem Compound</Menu>
-				<Description>PubChem chemical compound records that cite the current articles. These references are taken from those provided on submitted PubChem chemical substance records. Multiple substance records may contribute to the PubChem compound record.</Description>
-				<DbTo>pccompound</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pccompound_mesh</Name>
-				<Menu>PubChem Compound (MeSH Keyword)</Menu>
-				<Description>PubChem chemical compound records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.</Description>
-				<DbTo>pccompound</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pccompound_publisher</Name>
-				<Menu>PubChem Compound (Publisher)</Menu>
-				<Description>Link to publisher deposited structures in the PubChem Compound database.</Description>
-				<DbTo>pccompound</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pcsubstance</Name>
-				<Menu>PubChem Substance Links</Menu>
-				<Description>PubChem chemical substance records that cite the current articles. These references are taken from those provided on submitted PubChem chemical substance records.</Description>
-				<DbTo>pcsubstance</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pcsubstance_bookrecords</Name>
-				<Menu>PubChem Substance (from Bookshelf)</Menu>
-				<Description>Structures in the PubChem Substance database in this citation</Description>
-				<DbTo>pcsubstance</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pcsubstance_mesh</Name>
-				<Menu>PubChem Substance (MeSH Keyword)</Menu>
-				<Description>PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.</Description>
-				<DbTo>pcsubstance</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pcsubstance_publisher</Name>
-				<Menu>PubChem Substance (Publisher)</Menu>
-				<Description>Publisher deposited structures in the PubChem Compound database that are reported in the current articles.</Description>
-				<DbTo>pcsubstance</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pmc</Name>
-				<Menu>PMC Links</Menu>
-				<Description>Free full-text versions of the current articles in the PubMed Central database.</Description>
-				<DbTo>pmc</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pmc_bookrecords</Name>
-				<Menu>References in PMC for this Bookshelf citation</Menu>
-				<Description>Full text of articles in PubMed Central cited in this record</Description>
-				<DbTo>pmc</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pmc_embargo</Name>
-				<Menu></Menu>
-				<Description>Embargoed PMC article associated with PubMed</Description>
-				<DbTo>pmc</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pmc_local</Name>
-				<Menu></Menu>
-				<Description>Free full text articles in PMC</Description>
-				<DbTo>pmc</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pmc_refs</Name>
-				<Menu>Cited in PMC</Menu>
-				<Description>Full-text articles in the PubMed Central Database that cite the current articles.</Description>
-				<DbTo>pmc</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_popset</Name>
-				<Menu>PopSet Links</Menu>
-				<Description>Sets of sequences from population and evolutionary genetic studies in the PopSet database reported in the current articles.</Description>
-				<DbTo>popset</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_probe</Name>
-				<Menu>Probe Links</Menu>
-				<Description>Molecular reagents in the Probe database that cite the current articles. References in Probe are provided by submitters of the data.</Description>
-				<DbTo>probe</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_protein</Name>
-				<Menu>Protein Links</Menu>
-				<Description>Protein translation features of primary database (GenBank) nucleotide records reported in the current articles as well as Reference Sequences (RefSeqs) that include the articles as references.</Description>
-				<DbTo>protein</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_protein_refseq</Name>
-				<Menu>Protein (RefSeq) Links</Menu>
-				<Description>NCBI protein Reference Sequences (RefSeqs) that are cited in the current articles, included in the corresponding Gene Reference into Function, or that include the PubMed articles as references.</Description>
-				<DbTo>protein</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_protein_weighted</Name>
-				<Menu>Protein (Weighted) Links</Menu>
-				<Description>Protein records associated with the current articles through related Gene database records. These are the related sequences on the Gene record that are added manually by NCBI.</Description>
-				<DbTo>protein</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_proteinclusters</Name>
-				<Menu>Protein Cluster Links</Menu>
-				<Description>Clusters of related proteins from the Protein Clusters database that cite the current articles. Sources of references in Protein Clusters include the associated Gene and Conserved Domain records as well as NCBI added citations.</Description>
-				<DbTo>proteinclusters</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pubmed</Name>
-				<Menu>Related Citations</Menu>
-				<Description>Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.</Description>
-				<DbTo>pubmed</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pubmed_alsoviewed</Name>
-				<Menu>Articles frequently viewed together</Menu>
-				<Description>&lt;p&gt;Links to additional articles that others frequently viewed together with your selection.&lt;/p&gt;&lt;p&gt;&lt;i&gt;An experimental new feature from PubMed Labs&lt;/i&gt;.&lt;/p&gt;</Description>
-				<DbTo>pubmed</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pubmed_bookrecords</Name>
-				<Menu>References for this Bookshelf citation</Menu>
-				<Description>PubMed abstracts for articles cited in this record</Description>
-				<DbTo>pubmed</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pubmed_pmh_cited</Name>
-				<Menu>Clinical Trial Review</Menu>
-				<Description>PubMed records cited in PubMed Health systematic reviews</Description>
-				<DbTo>pubmed</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_pubmed_refs</Name>
-				<Menu>References for PMC Articles</Menu>
-				<Description>Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.</Description>
-				<DbTo>pubmed</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_snp</Name>
-				<Menu>SNP Links</Menu>
-				<Description>Nucleotide polymorphism records from dbSNP that have current articles as submitter-provided references.</Description>
-				<DbTo>snp</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_snp_cited</Name>
-				<Menu>SNP (Cited)</Menu>
-				<Description>Nucleotide polymorphism records from dbSNP that have NCBI dbSNP identifiers reported in the PubMed abstract of the current articles.</Description>
-				<DbTo>snp</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_sra</Name>
-				<Menu>SRA Links</Menu>
-				<Description>Massively-parallel sequencing project data in the Short Read Archive (SRA) that are reported in the current articles.</Description>
-				<DbTo>sra</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_structure</Name>
-				<Menu>Structure Links</Menu>
-				<Description>Three-dimensional structure records in the NCBI Structure database for data reported in the current articles.</Description>
-				<DbTo>structure</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_taxonomy_entrez</Name>
-				<Menu>Taxonomy via GenBank</Menu>
-				<Description>Taxonomy records associated with the current articles through taxonomic information on related molecular database records (Nucleotide, Protein, Gene, SNP, Structure).</Description>
-				<DbTo>taxonomy</DbTo>
-			</Link>
-			<Link>
-				<Name>pubmed_unigene</Name>
-				<Menu>UniGene Links</Menu>
-				<Description>UniGene clusters of expressed sequences that are associated with the current articles through references on the clustered sequence records and related Gene records.</Description>
-				<DbTo>unigene</DbTo>
-			</Link>
-		</LinkList>
-	</DbInfo>
-
-</eInfoResult>
-
--- a/tool_dependencies.xml	Sat Oct 31 12:44:54 2015 -0400
+++ b/tool_dependencies.xml	Mon Nov 02 12:59:23 2015 -0500
@@ -4,6 +4,6 @@
     <environment_variable action="set_to" name="NCBI_EUTILS_CONTACT">/please set the administrator's contact email in the corresponding env.sh file/</environment_variable>
   </set_environment>
   <package name="biopython" version="1.66">
-    <repository changeset_revision="ef89610ae47c" name="package_biopython_1_66" owner="biopython" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="ef89610ae47c" name="package_biopython_1_66" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>