# HG changeset patch
# User peterjc
# Date 1417193377 18000
# Node ID e12fd6f5992c70f4a0b41794aba0a816393c1349
# Parent  42bca649ec44aa382a6b058c1d73813410e94283
Uploaded v0.0.12, simplified XML, embed citation.

diff -r 42bca649ec44 -r e12fd6f5992c test-data/MID4_GLZRM4E04_rnd30_fclip.pair_sample_N5.sff
Binary file test-data/MID4_GLZRM4E04_rnd30_fclip.pair_sample_N5.sff has changed
diff -r 42bca649ec44 -r e12fd6f5992c test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff
Binary file test-data/MID4_GLZRM4E04_rnd30_frclip.pair_sample_N5.sff has changed
diff -r 42bca649ec44 -r e12fd6f5992c test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff
Binary file test-data/MID4_GLZRM4E04_rnd30_frclip.sample_N5.sff has changed
diff -r 42bca649ec44 -r e12fd6f5992c test-data/MID4_GLZRM4E04_rnd30_frclip.seq_composition.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/MID4_GLZRM4E04_rnd30_frclip.seq_composition.tabular	Fri Nov 28 11:49:37 2014 -0500
@@ -0,0 +1,5 @@
+Letter	Count	Percentage
+A	1733	27.68
+C	1267	20.24
+G	1551	24.78
+T	1709	27.30
diff -r 42bca649ec44 -r e12fd6f5992c tools/seq_primer_clip/README.rst
--- a/tools/seq_primer_clip/README.rst	Wed Nov 20 12:10:15 2013 -0500
+++ b/tools/seq_primer_clip/README.rst	Fri Nov 28 11:49:37 2014 -0500
@@ -1,7 +1,7 @@
 Galaxy tool to primer clip (trim) FASTA, FASTQ or SFF reads
 ===========================================================
 
-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 (MIT licence).
 
@@ -23,18 +23,19 @@
 
 There are just two files to install:
 
-* seq_primer_clip.py (the Python script)
-* seq_primer_clip.xml (the Galaxy tool definition)
+* ``seq_primer_clip.py`` (the Python script)
+* ``seq_primer_clip.xml`` (the Galaxy tool definition)
 
-The suggested location is a new tools/seq_primer_clip folder. You will also
-need to modify the tools_conf.xml file to tell Galaxy to offer the tool::
+The suggested location is a new ``tools/seq_primer_clip/`` folder. You will
+also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the
+tool::
 
   <tool file="seq_primer_clip/seq_primer_clip.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_primer_clip
+    $ ./run_tests.sh -id seq_primer_clip
 
 You will also need to install Biopython 1.54 or later. That's it.
 
@@ -62,6 +63,8 @@
         - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
         - Renamed folder and adopted README.rst naming.
 v0.0.11 - Correct automated dependency definition.
+v0.0.12 - Simplified XML to apply input format to output data.
+        - Tool definition now embeds citation information.
 ======= ======================================================================
 
 
diff -r 42bca649ec44 -r e12fd6f5992c tools/seq_primer_clip/seq_primer_clip.xml
--- a/tools/seq_primer_clip/seq_primer_clip.xml	Wed Nov 20 12:10:15 2013 -0500
+++ b/tools/seq_primer_clip/seq_primer_clip.xml	Fri Nov 28 11:49:37 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.10">
+<tool id="seq_primer_clip" name="Primer clip sequences" version="0.0.12">
     <description>Trim off 5' or 3' primers</description>
     <requirements>
         <requirement type="package" version="1.62">biopython</requirement>
@@ -28,18 +28,7 @@
         <param name="min_len" type="integer" label="Minimum length for (clipped) sequences " value="1"/>
     </inputs>
     <outputs>
-        <data name="output_file" format="data" label="$primer_type primer clipped">
-            <!-- TODO - Replace this with format="input:input_fastq" if/when that works -->
-            <change_format>
-                <when input_dataset="input_file" attribute="extension" value="sff" format="sff" />
-                <when input_dataset="input_file" attribute="extension" value="fasta" format="fasta" />
-                <when input_dataset="input_file" attribute="extension" value="fastq" format="fastq" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsanger" format="fastqsanger" />
-                <when input_dataset="input_file" attribute="extension" value="fastqsolexa" format="fastqsolexa" />
-                <when input_dataset="input_file" attribute="extension" value="fastqillumina" format="fastqillumina" />
-                <when input_dataset="input_file" attribute="extension" value="fastqcssanger" format="fastqcssanger" />
-            </change_format>
-        </data>
+        <data name="output_file" format="input" metadata_source="input_file" label="$primer_type primer clipped"/>
     </outputs>
     <tests>
         <test>
@@ -140,4 +129,7 @@
 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_primer_clip 
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp163</citation>
+    </citations>
 </tool>
diff -r 42bca649ec44 -r e12fd6f5992c tools/seq_primer_clip/tool_dependencies.xml
--- a/tools/seq_primer_clip/tool_dependencies.xml	Wed Nov 20 12:10:15 2013 -0500
+++ b/tools/seq_primer_clip/tool_dependencies.xml	Fri Nov 28 11:49:37 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>