# HG changeset patch
# User iuc
# Date 1442696745 14400
# Node ID b5066aa77feaab288a7f3807f443ad5c5befbb62
# Parent  62479bdcc059528ca11d9f2f443bd7b8581315ae
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit f7d83adb11624763b9b113f938a1d5f311c8f9fa-dirty

diff -r 62479bdcc059 -r b5066aa77fea hmmconvert.xml
--- a/hmmconvert.xml	Tue May 12 15:04:26 2015 -0400
+++ b/hmmconvert.xml	Sat Sep 19 17:05:45 2015 -0400
@@ -20,10 +20,10 @@
     </param>
   </inputs>
   <outputs>
-    <data format="hmmer3" name="output" label="$msafile.name">
+    <data format="hmm3" name="output" label="$msafile.name">
       <change_format>
-        <when input="format" value="-a" format="hmmer3"/>
-        <when input="format" value="-2" format="hmmer2"/>
+        <when input="format" value="-a" format="hmm3"/>
+        <when input="format" value="-2" format="hmm2"/>
       </change_format>
     </data>
   </outputs>
diff -r 62479bdcc059 -r b5066aa77fea hmmfetch.xml
--- a/hmmfetch.xml	Tue May 12 15:04:26 2015 -0400
+++ b/hmmfetch.xml	Sat Sep 19 17:05:45 2015 -0400
@@ -15,7 +15,7 @@
     <param name="keyfile" type="data" format="tabular,txt" label="List of HMM names to extract"/>
   </inputs>
   <outputs>
-    <data format="hmmer3" name="output" label="Selected HMM Models from $hmmfile.name">
+    <data format="hmm3" name="output" label="Selected HMM Models from $hmmfile.name">
     </data>
   </outputs>
   <tests>
diff -r 62479bdcc059 -r b5066aa77fea macros.xml
--- a/macros.xml	Tue May 12 15:04:26 2015 -0400
+++ b/macros.xml	Sat Sep 19 17:05:45 2015 -0400
@@ -392,10 +392,11 @@
         help="(--w_length)" optional="True" type="integer" />
   </xml>
   <xml name="input_hmm">
-    <param name="hmmfile" type="data" label="HMM model" format="hmmer2,hmmer3"/>
+    <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
   </xml>
   <xml name="input_msa">
-    <param name="msafile" type="data" label="MSA File" format="stockholm"/>
+    <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta"
+      help="in Stockholm, Clustal, or Fasta format. While this tool accepts fasta, please ensure that the sequences are not unaligned"/>
   </xml>