# HG changeset patch
# User guerler
# Date 1596220275 14400
# Node ID 691d8f7c078c00313364c836a9c614ba579a3147
# Parent  35dbd62871b02f47343d37ae4aa07b05c8e6c602
"planemo upload commit 3002402473e9f6dcdac5bfb4013cd2d81884a938-dirty"

diff -r 35dbd62871b0 -r 691d8f7c078c hhblits.xml
--- a/hhblits.xml	Fri Jul 31 00:14:10 2020 -0400
+++ b/hhblits.xml	Fri Jul 31 14:31:15 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="hhblits" name="HH-blits" version="0.1.0" python_template_version="3.5">
+<tool id="hhblits" name="HHblits" version="0.1.0" python_template_version="3.5">
     <description>itererative protein sequence searching</description>
     <requirements>
         <requirement type="package" version="3.2.0">hhsuite</requirement>
@@ -8,17 +8,21 @@
         link '$hhm_ffindex' hhdb_hhm.ffindex &&
         link '$cs219_ffdata' hhdb_cs219.ffdata &&
         link '$cs219_ffindex' hhdb_cs219.ffindex &&
-        hhblits -n '$n' -e '$e' -i '$input' -d hhdb -o '$output'
+        $method -n '$n' -e '$e' -i '$input' -d hhdb -o '$output'
     ]]></command>
     <inputs>
         <param format="data" name="input" type="data" label="Query Sequence" help="Single sequence or multiple sequence alignment (MSA)
-                in a3m, a2m, or FASTA format, or HMM in hhm format (-i)"/>
-        <param format="data" name="hhm_ffindex" type="data" label="HHM Index file" help="Database file ending with 'hhm.ffindex'"/>
-        <param format="data" name="hhm_ffdata" type="data" label="HHM Data file" help="Database file ending with 'hhm.ffdata'"/>
-        <param format="data" name="cs219_ffindex" type="data" label="cs219 Index file" help="Database file ending with 'cs219.ffindex'"/>
-        <param format="data" name="cs219_ffdata" type="data" label="cs219 Data file" help="Database file ending with 'cs219.ffdata'"/>
-        <param name="n" type="integer" label="Number of Iterations (-n)" value="2" min="1" max="8"/>
-        <param name="e" type="float" label="E-value cutoff for inclusion in result alignment (-e)" value="0.001" min="0" max="1"/>
+                in a3m, a2m, or FASTA format, or HMM in hhm format. (-i)"/>
+        <param format="data" name="hhm_ffindex" type="data" label="HHM Index file" help="Database file ending with 'hhm.ffindex'."/>
+        <param format="data" name="hhm_ffdata" type="data" label="HHM Data file" help="Database file ending with 'hhm.ffdata'."/>
+        <param format="data" name="cs219_ffindex" type="data" label="cs219 Index file" help="Database file ending with 'cs219.ffindex'."/>
+        <param format="data" name="cs219_ffdata" type="data" label="cs219 Data file" help="Database file ending with 'cs219.ffdata'."/>
+        <param name="n" type="integer" label="Number of Iterations. (-n)" value="2" min="1" max="8"/>
+        <param name="e" type="float" label="E-value cutoff for inclusion in result alignment. (-e)" value="0.001" min="0" max="1"/>
+        <param name="method" type="select" label="Search Method" help="Select the search method.">
+            <option value="hhblits" selected="true">HHblits</option>
+            <option value="hhsearch">HHsearch</option>
+        </param>
     </inputs>
     <outputs>
         <data format="data" name="output" />
@@ -35,7 +39,7 @@
     </tests>
     <help><![CDATA[
 HMM-HMM-based lightning-fast iterative sequence search
-HHblits is a sensitive, general-purpose, iterative sequence search tool that represents
+HHblits and HHsearch is a sensitive, general-purpose, iterative sequence search tool that represents
 both query and database sequences by HMMs. You can search HHblits databases starting
 with a single query sequence, a multiple sequence alignment (MSA), or an HMM. HHblits
 prints out a ranked list of database HMMs/MSAs and can also generate an MSA by merging