changeset 1:e779d71f871a draft

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

--- a/macros.xml	Sat Jun 25 15:06:44 2016 -0400
+++ b/macros.xml	Mon Nov 14 15:11:29 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>

--- a/readme.rst	Sat Jun 25 15:06:44 2016 -0400
+++ b/readme.rst	Mon Nov 14 15:11:29 2016 -0500
@@ -29,6 +29,7 @@
 History
 =======
 
+* v0.1.1    - hmmscan: add the possibility to scan a built-in hmm profile database
 * v0.1      - Initial public release
 
 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/hmm_database.loc.sample	Mon Nov 14 15:11:29 2016 -0500
@@ -0,0 +1,10 @@
+#This is a sample file that enables the hmmer tools to find the HMM databases
+#You will need to create these data files and then create
+#a hmm_database.loc file similar to this one (store it in this directory)
+#that points to the directories in which those files are stored.
+#The hmm_database_indices.loc file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <display_name>   <file_base_path>
+#
+#So, for example:
+#pfam_a	Pfam-a	/data/db/pfam/Pfam-A.hmm

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Nov 14 15:11:29 2016 -0500
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of indexes in the HMM database format -->
+    <table name="hmm_database" comment_char="#">
+        <columns>value, name, db_path</columns>
+        <file path="tool-data/hmm_database.loc" />
+    </table>
+</tables>