Remove stdio

Empty CDATA is an issue. galaxyproject/planemo#362
galaxyproject · Oct 31, 2015 · 98f82c5 · 98f82c5
1 parent 8c8ca5c
commit 98f82c5
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Showing 9 changed files with 3 additions and 10 deletions.
diff --git a/tools/ncbi_entrez_eutils/ecitmatch.xml b/tools/ncbi_entrez_eutils/ecitmatch.xml
@@ -5,7 +5,6 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python ecitmatch.py --version</version_command>
   <command detect_errors="aggressive" detect_errors="aggressive" interpreter="python"><![CDATA[ecitmatch.py
 

diff --git a/tools/ncbi_entrez_eutils/efetch.xml b/tools/ncbi_entrez_eutils/efetch.xml
@@ -5,7 +5,6 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python efetch.py --version</version_command>
   <command detect_errors="aggressive" interpreter="python"><![CDATA[efetch.py
 $db.db_select

diff --git a/tools/ncbi_entrez_eutils/egquery.xml b/tools/ncbi_entrez_eutils/egquery.xml
@@ -5,7 +5,6 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python egquery.py --version</version_command>
   <command detect_errors="aggressive" interpreter="python"><![CDATA[egquery.py
 "$term"
@@ -33,7 +32,7 @@
   <tests>
     <test>
       <param name="term" value="bacteriophage"/>
-      <output name="default" file="egquery.1.xml" compare="sim_size"/>
+      <output name="default" file="egquery.1.xml" compare="contains"/>
     </test>
   </tests>
   <help><![CDATA[

diff --git a/tools/ncbi_entrez_eutils/einfo.xml b/tools/ncbi_entrez_eutils/einfo.xml
@@ -5,7 +5,6 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python einfo.py --version</version_command>
   <command detect_errors="aggressive" interpreter="python"><![CDATA[einfo.py
 --db $db_select

diff --git a/tools/ncbi_entrez_eutils/elink.xml b/tools/ncbi_entrez_eutils/elink.xml
@@ -5,7 +5,6 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python elink.py --version</version_command>
   <command detect_errors="aggressive" interpreter="python"><![CDATA[elink.py
 #if $cmd.cmd_select in ('neighbor', 'neighbor_score', 'neighbor_history'):

diff --git a/tools/ncbi_entrez_eutils/epost.xml b/tools/ncbi_entrez_eutils/epost.xml
@@ -5,7 +5,6 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python epost.py --version</version_command>
   <command detect_errors="aggressive" interpreter="python"><![CDATA[epost.py
 $db_select

diff --git a/tools/ncbi_entrez_eutils/esearch.xml b/tools/ncbi_entrez_eutils/esearch.xml
@@ -5,7 +5,6 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python esearch.py --version</version_command>
   <command detect_errors="aggressive" interpreter="python"><![CDATA[esearch.py
 $db_select

diff --git a/tools/ncbi_entrez_eutils/esummary.xml b/tools/ncbi_entrez_eutils/esummary.xml
@@ -5,7 +5,6 @@
     <import>macros.xml</import>
   </macros>
   <expand macro="requirements"/>
-  <expand macro="stdio"/>
   <version_command>python esummary.py --version</version_command>
   <command detect_errors="aggressive" interpreter="python"><![CDATA[esummary.py
 $db_select

diff --git a/tools/ncbi_entrez_eutils/macros.xml b/tools/ncbi_entrez_eutils/macros.xml
@@ -7,7 +7,8 @@
 --admin_email $admin_emails
   </token>
   <!--  TODO: citation -->
-  <token name="@REFERENCES@"><![CDATA[]]></token>
+  <token name="@REFERENCES@"><![CDATA[
+  ]]></token>
   <token name="@DISCLAIMER@"><![CDATA[
 Usage Guidelines and Requirements
 =================================