# HG changeset patch
# User iuc
# Date 1479154242 18000
# Node ID 6d44e7f6513feccb734c16dd517effeb1eaf26c4
# Parent dca536c5cca5e8148c5e0447b72d06b5b1dcadbf
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
diff -r dca536c5cca5 -r 6d44e7f6513f macros.xml
--- a/macros.xml Sat Jun 25 15:05:21 2016 -0400
+++ b/macros.xml Mon Nov 14 15:10:42 2016 -0500
@@ -391,6 +391,32 @@
+
+#if $input_hmm_conditional.input_hmm_source == "history":
+ '$input_hmm_conditional.hmmfile'
+#else:
+ '$input_hmm_conditional.index.fields.db_path'
+#end if
+
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@@ -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 `__.
+posted on the `developer's blog `__.
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/
]]>
diff -r dca536c5cca5 -r 6d44e7f6513f readme.rst
--- a/readme.rst Sat Jun 25 15:05:21 2016 -0400
+++ b/readme.rst Mon Nov 14 15:10:42 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
diff -r dca536c5cca5 -r 6d44e7f6513f tool-data/hmm_database.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/hmm_database.loc.sample Mon Nov 14 15:10:42 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):
+#
+#
+#
+#So, for example:
+#pfam_a Pfam-a /data/db/pfam/Pfam-A.hmm
diff -r dca536c5cca5 -r 6d44e7f6513f tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Mon Nov 14 15:10:42 2016 -0500
@@ -0,0 +1,7 @@
+
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+