# HG changeset patch
# User peterjc
# Date 1416576739 18000
# Node ID 9c2b10d7b8ac0294a66a5d858f1e9768ef084b6a
# Parent  bedfe8f3d3fbda104ffae2e61faa78b8a88292dd
Uploaded v0.0.9, embeds citation, better naming of outputs

diff -r bedfe8f3d3fb -r 9c2b10d7b8ac tools/seq_select_by_id/README.rst
--- a/tools/seq_select_by_id/README.rst	Wed Nov 20 12:13:14 2013 -0500
+++ b/tools/seq_select_by_id/README.rst	Fri Nov 21 08:32:19 2014 -0500
@@ -1,7 +1,7 @@
 Galaxy tool to select FASTA, QUAL, FASTQ or SFF sequences by ID
 ===============================================================
 
-This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2014 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -36,20 +36,20 @@
 
 There are just two files to install to use this tool from within Galaxy:
 
-* seq_select_by_id.py (the Python script)
-* seq_select_by_id.xml (the Galaxy tool definition)
+* ``seq_select_by_id.py`` (the Python script)
+* ``seq_select_by_id.xml`` (the Galaxy tool definition)
 
-The suggested location is a dedicated tools/seq_select_by_id folder.
+The suggested location is a dedicated ``tools/seq_select_by_id`` folder.
 
-You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
 tool. One suggested location is in the filters section. Simply add the line::
 
     <tool file="seq_select_by_id/seq_select_by_id.xml" />
 
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    $ ./run_functional_tests.sh -id seq_select_by_id
+    $ ./run_tests.sh -id seq_select_by_id
 
 You will also need to install Biopython 1.54 or later. That's it.
 
@@ -73,7 +73,10 @@
         - Fixed Biopython dependency setup.
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
         - Renamed folder and adopted README.rst naming.
-v0.0.8  - Corrected automated dependency definition
+v0.0.8  - Corrected automated dependency definition.
+v0.0.9  - Simplified XML to apply input format to output data.
+        - Tool definition now embeds citation information.
+        - Include input dataset name in output dataset names.
 ======= ======================================================================
 
 
diff -r bedfe8f3d3fb -r 9c2b10d7b8ac tools/seq_select_by_id/seq_select_by_id.xml
--- a/tools/seq_select_by_id/seq_select_by_id.xml	Wed Nov 20 12:13:14 2013 -0500
+++ b/tools/seq_select_by_id/seq_select_by_id.xml	Fri Nov 21 08:32:19 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.6">
+<tool id="seq_select_by_id" name="Select sequences by ID" version="0.0.9">
     <description>from a tabular file</description>
     <requirements>
         <requirement type="package" version="1.62">biopython</requirement>
@@ -19,17 +19,7 @@
         <param name="column" type="data_column" data_ref="input_tabular" multiple="False" numerical="False" label="Column containing sequence identifiers"/>
     </inputs>
     <outputs>
-        <data name="output_file" format="fasta" label="Selected sequences">
-            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-            <change_format>
-                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-            </change_format>
-        </data>
+        <data name="output_file" format="input" metadata_source="input_file" label="Selected sequences from $input_file.name"/>
     </outputs>
     <tests>
         <test>
@@ -69,4 +59,8 @@
 This tool is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
 </tool>
diff -r bedfe8f3d3fb -r 9c2b10d7b8ac tools/seq_select_by_id/tool_dependencies.xml
--- a/tools/seq_select_by_id/tool_dependencies.xml	Wed Nov 20 12:13:14 2013 -0500
+++ b/tools/seq_select_by_id/tool_dependencies.xml	Fri Nov 21 08:32:19 2014 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="biopython" version="1.62">
-        <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>