diff macros.xml @ 1:855e2b978e3a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde

--- a/macros.xml	Sat Jun 25 15:05:37 2016 -0400
+++ b/macros.xml	Mon Nov 14 15:10:53 2016 -0500
@@ -391,6 +391,32 @@
     <param name="w_length" label="Window Length"
         help="(--w_length)" optional="True" type="integer" />
   </xml>
+  <token name="@INPUTHMMCHOICE@">
+#if $input_hmm_conditional.input_hmm_source == "history":
+    '$input_hmm_conditional.hmmfile'
+#else:
+    '$input_hmm_conditional.index.fields.db_path'
+#end if
+  </token>
+  <xml name="input_hmm_choice">
+    <conditional name="input_hmm_conditional">
+      <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" >
+        <option value="indexed" selected="True">Use a built-in HMM model database</option>
+        <option value="history">Use a HMM database from history</option>
+      </param>
+      <when value="indexed">
+        <param name="index" type="select" label="Select a HMM model database" help="If your database of interest is not listed, contact the Galaxy administrator">
+          <options from_data_table="hmm_database">
+            <filter type="sort_by" column="2"/>
+            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
+      </when>  <!-- history -->
+    </conditional>  <!-- input_hmm_conditional -->
+  </xml>
   <xml name="input_hmm">
     <param name="hmmfile" type="data" label="HMM model" format="hmm2,hmm3"/>
   </xml>
@@ -524,7 +550,7 @@
 **Advanced Documentation**
 
 A more detailed look at the internals of the various filter pipelines was
-posted on the `developer's blog <http://selab.janelia.org/people/eddys/blog/?p=508>`__.
+posted on the `developer's blog <https://cryptogenomicon.org/2011/09/19/hmmer3-is-stubborn/>`__.
 The information posted there may be useful to those who are struggling with
 poor-scoring sequences.
 
@@ -1041,7 +1067,7 @@
 Attribution
 -----------
 
-This Galaxy tool relies on HMMER3_ from http://hmmer.janelia.org/
+This Galaxy tool relies on HMMER3_
 Internally the software is cited as:
 
 ::
@@ -1056,7 +1082,7 @@
 documentation is copied from the HMMER3 documentation.
 
 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
-.. _HMMER3: http://hmmer.janelia.org/
+.. _HMMER3: http://hmmer.org/
 
 
   ]]></token>