diff nhmmer.xml @ 3:c8e81e43bff1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6

--- a/nhmmer.xml	Wed Apr 04 14:01:13 2018 -0400
+++ b/nhmmer.xml	Sat Apr 07 03:50:51 2018 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hmmer_nhmmer" name="nhmmer" version="@WRAPPER_VERSION@.0">
+<tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@">
   <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
   <macros>
     <import>macros.xml</import>
@@ -20,10 +20,10 @@
 @CPU@
 @SEED@
 
-$hmmfile
-$seqfile
-> $output
-      ]]></command>
+'$hmmfile'
+'$seqfile'
+> '$output'
+  ]]></command>
   <inputs>
     <expand macro="input_hmm" />
     <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
@@ -57,7 +57,9 @@
       <param name="seqfile" value="dna_target.fa"/>
       <expand macro="oformat_test" />
       <expand macro="seed_test" />
-      <output name="output" file="nhmmer.out" lines_diff="32"/>
+      <output name="output" file="nhmmer.out" lines_diff="10" />
+      <output name="tblout" file="nhmmer.out.tblout" lines_diff="10" />
+      <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10" />
     </test>
   </tests>
   <help><![CDATA[
@@ -85,6 +87,6 @@
 @SEED_HELP@
 
 @ATTRIBUTION@
-]]></help>
+  ]]></help>
   <expand macro="citation"/>
 </tool>