diff einfo.xml @ 2:df0df73c8bda draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_direct commit 1bd7defa5ac7ea1e619c519d719f5bd10452339b

--- a/einfo.xml	Sat Dec 17 20:44:55 2022 +0000
+++ b/einfo.xml	Sat May 18 20:23:10 2024 +0000
@@ -1,11 +1,11 @@
 <tool id="ncbi_entrez_direct_einfo" name="NCBI EInfo" version="@TOOL_VERSION@">
-  <description>fetch NCBI database metadata</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"/>
-  <version_command>einfo -version</version_command>
-  <command detect_errors="exit_code"><![CDATA[
+    <description>fetch NCBI database metadata</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <version_command>einfo -version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
       @ECONTACT@
       einfo
       #if str( $db.target ) == "dbs":
@@ -16,81 +16,81 @@
       > '${output_xml}'
       ]]>  
 </command>
-  <inputs>
-      <conditional name="db">
-          <param name="target" type="select" label="List DBs or Info on a DB">
-              <option value="db" selected="True">DB info</option>
-              <option value="dbs">List of DBs</option>
-          </param>
-          <when value="dbs"/>
-          <when value="db">
-              <param name="db" type="select" label="Choose your DB" argument="-db">
-                  <option value="annotinfo">annotinfo</option>
-                  <option value="assembly">assembly</option>
-                  <option value="bioproject">bioproject</option>
-                  <option value="biosample">biosample</option>
-                  <option value="biosystems">biosystems</option>
-                  <option value="blastdbinfo">blastdbinfo</option>
-                  <option value="books">books</option>
-                  <option value="cdd">cdd</option>
-                  <option value="clinvar">clinvar</option>
-                  <option value="clone">clone</option>
-                  <option value="dbvar">dbvar</option>
-                  <option value="gap">gap</option>
-                  <option value="gapplus">gapplus</option>
-                  <option value="gds">gds</option>
-                  <option value="gencoll">gencoll</option>
-                  <option value="gene">gene</option>
-                  <option value="genome">genome</option>
-                  <option value="geoprofiles">geoprofiles</option>
-                  <option value="grasp">grasp</option>
-                  <option value="gtr">gtr</option>
-                  <option value="homologene">homologene</option>
-                  <option value="medgen">medgen</option>
-                  <option value="mesh">mesh</option>
-                  <option value="ncbisearch">ncbisearch</option>
-                  <option value="nlmcatalog">nlmcatalog</option>
-                  <option value="nuccore">nuccore</option>
-                  <option value="nucest">nucest</option>
-                  <option value="nucgss">nucgss</option>
-                  <option value="nucleotide">nucleotide</option>
-                  <option value="omim">omim</option>
-                  <option value="orgtrack">orgtrack</option>
-                  <option value="pcassay">pcassay</option>
-                  <option value="pccompound">pccompound</option>
-                  <option value="pcsubstance">pcsubstance</option>
-                  <option value="pmc">pmc</option>
-                  <option value="popset">popset</option>
-                  <option value="probe">probe</option>
-                  <option value="protein">protein</option>
-                  <option value="proteinclusters">proteinclusters</option>
-                  <option value="pubmed">pubmed</option>
-                  <option value="pubmedhealth">pubmedhealth</option>
-                  <option value="seqannot">seqannot</option>
-                  <option value="snp">snp</option>
-                  <option value="sra">sra</option>
-                  <option value="structure">structure</option>
-                  <option value="taxonomy">taxonomy</option>
-                  <option value="unigene">unigene</option>
-              </param>
-          </when>
-      </conditional>
-  </inputs>
-  <outputs>
-    <data format="xml" name="output_xml"/>
-  </outputs>
-  <tests>
-    <test>
-      <param name="db|target" value="db"/>
-      <param name="db|db" value="sra"/>
-      <output name="output_xml">
-          <assert_contents>
-              <has_text_matching expression="SRA" />
-          </assert_contents>
-      </output>
-    </test>
-  </tests>
-  <help><![CDATA[
+    <inputs>
+        <conditional name="db">
+            <param name="target" type="select" label="List DBs or Info on a DB">
+                <option value="db" selected="True">DB info</option>
+                <option value="dbs">List of DBs</option>
+            </param>
+            <when value="dbs"/>
+            <when value="db">
+                <param argument="-db" type="select" label="Choose your DB">
+                    <option value="annotinfo">annotinfo</option>
+                    <option value="assembly">assembly</option>
+                    <option value="bioproject">bioproject</option>
+                    <option value="biosample">biosample</option>
+                    <option value="biosystems">biosystems</option>
+                    <option value="blastdbinfo">blastdbinfo</option>
+                    <option value="books">books</option>
+                    <option value="cdd">cdd</option>
+                    <option value="clinvar">clinvar</option>
+                    <option value="clone">clone</option>
+                    <option value="dbvar">dbvar</option>
+                    <option value="gap">gap</option>
+                    <option value="gapplus">gapplus</option>
+                    <option value="gds">gds</option>
+                    <option value="gencoll">gencoll</option>
+                    <option value="gene">gene</option>
+                    <option value="genome">genome</option>
+                    <option value="geoprofiles">geoprofiles</option>
+                    <option value="grasp">grasp</option>
+                    <option value="gtr">gtr</option>
+                    <option value="homologene">homologene</option>
+                    <option value="medgen">medgen</option>
+                    <option value="mesh">mesh</option>
+                    <option value="ncbisearch">ncbisearch</option>
+                    <option value="nlmcatalog">nlmcatalog</option>
+                    <option value="nuccore">nuccore</option>
+                    <option value="nucest">nucest</option>
+                    <option value="nucgss">nucgss</option>
+                    <option value="nucleotide">nucleotide</option>
+                    <option value="omim">omim</option>
+                    <option value="orgtrack">orgtrack</option>
+                    <option value="pcassay">pcassay</option>
+                    <option value="pccompound">pccompound</option>
+                    <option value="pcsubstance">pcsubstance</option>
+                    <option value="pmc">pmc</option>
+                    <option value="popset">popset</option>
+                    <option value="probe">probe</option>
+                    <option value="protein">protein</option>
+                    <option value="proteinclusters">proteinclusters</option>
+                    <option value="pubmed">pubmed</option>
+                    <option value="pubmedhealth">pubmedhealth</option>
+                    <option value="seqannot">seqannot</option>
+                    <option value="snp">snp</option>
+                    <option value="sra">sra</option>
+                    <option value="structure">structure</option>
+                    <option value="taxonomy">taxonomy</option>
+                    <option value="unigene">unigene</option>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="xml" name="output_xml"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="db|target" value="db"/>
+            <param name="db|db" value="sra"/>
+            <output name="output_xml">
+                <assert_contents>
+                    <has_text_matching expression="SRA"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
 NCBI Entrez EInfo
 =================
 
@@ -100,5 +100,5 @@
 
 @DISCLAIMER@
       ]]></help>
-  <expand macro="citations"/>
+    <expand macro="citations"/>
 </tool>