diff elink.xml @ 1:127515819562 draft

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 12:58:21 -0500
parents ffc6d6234c8a
children 0ea9815942d2
line wrap: on
line diff
--- a/elink.xml	Sat Oct 31 12:44:05 2015 -0400
+++ b/elink.xml	Mon Nov 02 12:58:21 2015 -0500
@@ -5,13 +5,12 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python elink.py --version</version_command>
-  <command interpreter="python"><![CDATA[elink.py
+  <command detect_errors="aggressive" interpreter="python"><![CDATA[elink.py
 #if $cmd.cmd_select in ('neighbor', 'neighbor_score', 'neighbor_history'):
-$cmd.db_select_to
+    $cmd.db_select_to
 #else:
-"none"
+    "none"
 #end if
 
 $db_select_from
@@ -27,53 +26,7 @@
 
 > $default]]></command>
   <inputs>
-    <param name="db_select_from" type="select" label="From 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>
+    <expand macro="dbselect" name="db_select_from" label="From NCBI Database" />
     <conditional name="cmd">
       <param name="cmd_select" type="select" label="ELink command to execute">
         <option value="neighbor">Neighbor: Fetch a set of UIDs in DB linked to input UIDs in DBFROM</option>
@@ -87,16 +40,16 @@
         <option value="prlinks">Provider Links: List the primary LinkOut provider for each input UID</option>
       </param>
       <when value="neighbor">
-        <expand macro="db_select_to"/>
+        <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
       </when>
       <when value="neighbor_score">
-        <expand macro="db_select_to"/>
+        <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
       </when>
       <when value="neighbor_history">
-        <expand macro="db_select_to"/>
+        <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
       </when>
       <when value="acheck">
-        <expand macro="db_select_to"/>
+        <expand macro="dbselect" name="db_select_to" label="To NCBI Database" />
       </when>
       <when value="ncheck"/>
       <when value="lcheck"/>