Mercurial > repos > iuc > ncbi_eutils_ecitmatch

diff macros.xml @ 1:eb431e2636df 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 12:58:37 -0500
parents f1590b9068bd
children 165996bbfd94
line wrap: on
line diff
--- a/macros.xml	Sat Oct 31 12:44:17 2015 -0400
+++ b/macros.xml	Mon Nov 02 12:58:37 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>