diff compalignp.xml @ 1:f3a318881b1b draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/compalignp/ commit 608bf2d6f11fe6dceaa0060f729bdbb66cfee867

--- a/compalignp.xml	Tue Jun 09 05:36:03 2015 -0400
+++ b/compalignp.xml	Sun Nov 12 06:10:42 2017 -0500
@@ -3,21 +3,17 @@
     <requirements>
         <requirement type="package" version="1.0">compalignp</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
-    </stdio>
-    <command>
+    <command detect_errors="aggressive">
 <![CDATA[
     compalignp
-        -t $rna_alignment_target
-        -r $rna_alignment_reference
+        -t '$rna_alignment_target'
+        -r '$rna_alignment_reference'
     > $output
 ]]>
     </command>
     <inputs>
-        <param format="clustalw,stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" />
-        <param format="clustalw,stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" />
+        <param format="clustal,stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" />
+        <param format="clustal,stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" />
     </inputs>
     <outputs>
         <data name="output" format="txt" />
@@ -31,6 +27,7 @@
     </tests>
     <help>
 <![CDATA[
+
 **compalignp**
 
 > Paranoia version of squids compalign. 
@@ -43,6 +40,6 @@
 ]]>
     </help>
 <citations>
-  <citation type="doi">10.1186/1748-7188-1-19</citation>
+    <citation type="doi">10.1186/1748-7188-1-19</citation>
 </citations>
 </tool>