# HG changeset patch
# User peterjc
# Date 1536158697 14400
# Node ID 4554fcd4ef6d410a09f4a3163dd1cafa12f3c882
# Parent  18fe33eb7775ffd921611013e195d73adb6efc4a
v0.0.6

diff -r 18fe33eb7775 -r 4554fcd4ef6d README.rst
--- a/README.rst	Wed Mar 14 12:46:57 2018 -0400
+++ b/README.rst	Wed Sep 05 10:44:57 2018 -0400
@@ -45,6 +45,27 @@
 in the ``tool-data/`` folder. Sample files are included which explain the
 tab-based format to use.
 
+For example, using https://doi.org/10.5281/zenodo.1406071 which is the
+database provided with Kodoja::
+
+    $ cd /mnt/shared/data/
+    $ mkdir kodojaDB_v1.0
+    $ cd kodojaDB_v1.0
+    $ wget https://zenodo.org/record/1406071/files/kodojaDB_v1.0.tar.gz
+    $ tar -zxvf kodojaDB_v1.0.tar.gz
+
+Then update your Galaxy configuration in ``tool-data/kraken_databases.loc``
+to add a line like this::
+
+    kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB
+
+And likewise update ``tool-data/kaiju_databases.loc`` with a line like::
+
+    kodojaDB_v1.0_kaiju(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB
+
+At the time of writing, reloading the ``*.loc`` files required restarting
+the Galaxy server.
+
 
 History
 =======
@@ -53,6 +74,9 @@
 Version Changes
 ------- ----------------------------------------------------------------------
 v0.0.0  - Initial release covering ``kodoja_search.py`` v0.0.3.
+v0.0.4  - Minor update to call ``kodoja_search.py`` v0.0.4.
+v0.0.6  - Minor update to call ``kodoja_search.py`` v0.0.6.
+        - Document installing the Kodoja databases from Zenodo.
 ======= ======================================================================
 
 
diff -r 18fe33eb7775 -r 4554fcd4ef6d kodoja_search.xml
--- a/kodoja_search.xml	Wed Mar 14 12:46:57 2018 -0400
+++ b/kodoja_search.xml	Wed Sep 05 10:44:57 2018 -0400
@@ -1,7 +1,7 @@
-<tool id="kodoja_search" name="Kodoja database search" version="0.0.0">
+<tool id="kodoja_search" name="Kodoja database search" version="0.0.6">
     <description>identify viruses from plant RNA sequencing data</description>
     <requirements>
-        <requirement type="package" version="0.0.3">kodoja</requirement>
+        <requirement type="package" version="0.0.6">kodoja</requirement>
     </requirements>
     <version_command>kodoja_search.py --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -53,7 +53,7 @@
             </options>
         </param>
         <conditional name="single_paired">
-            <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">
+            <param name="single_paired_selector" type="select" label="Single or paired reads">
                 <!-- TODO?
                 <option value="collection">Collection</option>
                 -->
@@ -102,8 +102,8 @@
 FASTQ/FASTA sequencing run by matching them against both
 Kraken and Kaiju databases.
 
-The main output is a five column tab-separated table as follows
-(tabular format in Galaxy):
+The main output is a tab-separated table as follows (tabular format in Galaxy)
+with the following columns:
 
 1. Species name
 2. Species NCBI taxonomy identifier (TaxID)
diff -r 18fe33eb7775 -r 4554fcd4ef6d test-data/krakenDB_test/accmap_file.tmp
diff -r 18fe33eb7775 -r 4554fcd4ef6d tool-data/kaiju_databases.loc.sample
--- a/tool-data/kaiju_databases.loc.sample	Wed Mar 14 12:46:57 2018 -0400
+++ b/tool-data/kaiju_databases.loc.sample	Wed Sep 05 10:44:57 2018 -0400
@@ -7,7 +7,7 @@
 #   files named ``kaiju_library.fmi``, ``names.dmp`` and
 #   ``nodes.dmp`` (the later being NCBI taxonomy files).
 #
-# e.g.
+# e.g. using the database provided with the kaiju-using tool
+# kodoja at https://doi.org/10.5281/zenodo.1406071
 #
-# plants_dec_2017(tab)Plants (December 2017)(tab)/mnt/shared/kaiju_db/plants_2017_12/
-#
+# kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kaiju), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/kaijuDB
diff -r 18fe33eb7775 -r 4554fcd4ef6d tool-data/kraken_databases.loc.sample
--- a/tool-data/kraken_databases.loc.sample	Wed Mar 14 12:46:57 2018 -0400
+++ b/tool-data/kraken_databases.loc.sample	Wed Sep 05 10:44:57 2018 -0400
@@ -8,7 +8,7 @@
 #   sub-directory named taxonomy containing files from the
 #   NCBI named ``names.dmp`` and ``nodes.dmp``
 #
-# e.g.
+# e.g. using the database provided with the kraken-using tool
+# kodoja at https://doi.org/10.5281/zenodo.1406071
 #
-# plants_dec_2017(tab)Plants (December 2017)(tab)/mnt/shared/kraken_db/plants_2017_12/
-#
+# kodojaDB_v1.0_kraken(tab)KodojaDB v1.0 (kraken), Sept 2018(tab)/mnt/shared/data/kodojaDB_v1.0/krakenDB