# HG changeset patch
# User peterjc
# Date 1438788485 14400
# Node ID 63ebe9726219d39a4a2caa808c47b2ff5727ab2b
# Parent  e59904c855ae3a1e508a406df55035817f2eec49
v0.0.11 move dependency to package_mira_3_4_1_1 etc

diff -r e59904c855ae -r 63ebe9726219 tools/mira3/README.rst
--- a/tools/mira3/README.rst	Wed Apr 30 07:21:57 2014 -0400
+++ b/tools/mira3/README.rst	Wed Aug 05 11:28:05 2015 -0400
@@ -30,10 +30,15 @@
 * ``mira.xml`` (the Galaxy tool definition)
 
 The suggested location is a new ``tools/mira3`` folder. You will also need to
-modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
-this to ``tools_conf.xml.sample`` in order to run any tests::
+modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding
+the line::
+ 
+  <tool file="mira3/mira.xml" />
 
-  <tool file="mira3/mira.xml" />
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+    $ ./run_tests -id mira_assembler
 
 You will also need to install MIRA, we used version 3.4.1.1. See:
 
@@ -77,6 +82,9 @@
         - Correct path issue in automated dependency installation.
 v0.0.10 - Added a functional test.
         - Updated URL for automated installation of MIRA v3.4.1.1
+v0.0.11 - Tool definition now embeds citation information.
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - MIRA 3.4.1.1 dependency now declared via dedicated Tool Shed package.
 ======= ======================================================================
 
 
@@ -89,21 +97,30 @@
 Development has now moved to a dedicated GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
 
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/empty_file.dat
+    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
+    ...
 
-Check this worked::
+or::
+
+    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
+    ...
 
-    $ tar -tzf mira3_wrapper.tar.gz
+To just build and check the tar ball, use::
+
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/mira3/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/empty_file.dat
+    test-data/tvc_contigs.fasta
+    test-data/tvc_mini.fastq
     tools/mira3/README.rst
-    tools/mira3/mira.xml
     tools/mira3/mira.py
+    tools/mira3/mira.xml
     tools/mira3/tool_dependencies.xml
-    test-data/tvc_mini.fastq
-    test-data/tvc_contigs.fasta
-    test-data/empty_file.dat
 
 
 Licence (MIT)
diff -r e59904c855ae -r 63ebe9726219 tools/mira3/mira.py
--- a/tools/mira3/mira.py	Wed Apr 30 07:21:57 2014 -0400
+++ b/tools/mira3/mira.py	Wed Aug 05 11:28:05 2015 -0400
@@ -9,7 +9,7 @@
 
 WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
 
-def stop_err(msg, err=1):
+def sys_exit(msg, err=1):
     sys.stderr.write(msg+"\n")
     sys.exit(err)
 
@@ -33,7 +33,7 @@
 
 mira_ver = get_version()
 if "V3.4." not in mira_ver:
-    stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
+    sys_exit("This wrapper is for MIRA V3.4, not %s" % mira_ver)
 if "-v" in sys.argv:
     print "MIRA wrapper version %s," % WRAPPER_VER
     print mira_ver
@@ -44,9 +44,9 @@
     n3 = (temp, name, name, name)
     f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
     if not os.path.isdir(f):
-        stop_err("Missing output folder")
+        sys_exit("Missing output folder")
     if not os.listdir(f):
-        stop_err("Empty output folder")
+        sys_exit("Empty output folder")
     missing = []
     for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
                      ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
@@ -58,7 +58,7 @@
         else:
             shutil.move(old, new)
     if missing:
-        stop_err("Missing output files: %s" % ", ".join(missing))
+        sys_exit("Missing output files: %s" % ", ".join(missing))
 
 def clean_up(temp, name):
     folder = "%s/%s_assembly" % (temp, name)
@@ -112,7 +112,7 @@
     handle.write(cmd + "\n")
     handle.close()
     clean_up(temp, name)
-    stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
+    sys_exit("Return error code %i from command:\n%s" % (return_code, cmd),
              return_code)
 handle.close()
 
diff -r e59904c855ae -r 63ebe9726219 tools/mira3/mira.xml
--- a/tools/mira3/mira.xml	Wed Apr 30 07:21:57 2014 -0400
+++ b/tools/mira3/mira.xml	Wed Aug 05 11:28:05 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.10">
+<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.11">
     <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
     <requirements>
         <requirement type="binary">mira</requirement>
@@ -189,4 +189,16 @@
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
 
     </help>
+    <citations>
+        <citation type="doi">10.7717/peerj.167</citation>
+        <citation type="bibtex">@ARTICLE{Chevreux1999-mira3,
+        author = {B. Chevreux and T. Wetter and S. Suhai},
+        year = {1999},
+        title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information},
+        journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)}
+        volume = {99},
+        pages = {45-56},
+        url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html}
+        }</citation>
+    </citations>
 </tool>
diff -r e59904c855ae -r 63ebe9726219 tools/mira3/tool_dependencies.xml
--- a/tools/mira3/tool_dependencies.xml	Wed Apr 30 07:21:57 2014 -0400
+++ b/tools/mira3/tool_dependencies.xml	Wed Aug 05 11:28:05 2015 -0400
@@ -1,27 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="MIRA" version="3.4.1.1">
-        <install version="1.0">
-            <actions>
-                <!-- Sourceforge doesn't offer nice clean download URLs which is a shame -->      
-                <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/Older%20releases/V3.4.0/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2</action>
-                <action type="move_directory_files">
-                    <source_directory>bin</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-Downloads MIRA v3.4 from Sourceforge, requesting Bastien's precompiled binaries
-for 64bit Linux (x86_64). He also has binaries for 32bit Linux, which we could
-use once the Galaxy installation framework allow that kind of flexibility.
-
-http://chevreux.org/projects_mira.html
-http://sourceforge.net/projects/mira-assembler/
-        </readme>
+        <repository changeset_revision="1c03c304fe69" name="package_mira_3_4_1_1" owner="peterjc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
-