# HG changeset patch
# User peterjc
# Date 1431443225 14400
# Node ID 174a38262fae11d357f9395a04b24b6d63793d3d
# Parent  a7c7f10488f5f8007ec9d3dce3ef1a554af703f0
planemo upload for repository https://github.com/peterjc/pico_galaxy/tools/align_back_trans commit 46f2d39f2030b3b0f883748f0c1a7c256b57ff34

diff -r a7c7f10488f5 -r 174a38262fae tools/align_back_trans/README.rst
--- a/tools/align_back_trans/README.rst	Fri Nov 28 11:32:34 2014 -0500
+++ b/tools/align_back_trans/README.rst	Tue May 12 11:07:05 2015 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to back-translate a protein alignment to nucleotides
 ================================================================
 
-This tool is copyright 2012-2014 by Peter Cock, The James Hutton Institute
+This tool is copyright 2012-2015 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below (MIT licence).
 
@@ -66,6 +66,9 @@
         - Fixed error message when sequence length not a multiple of three.
 v0.0.5  - More explicit error messages when seqences lengths do not match.
         - Tool definition now embeds citation information.
+v0.0.6  - Reorder XML elements (internal change only).
+        - Use ``format_source=...`` tag.
+        - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
 ======= ======================================================================
 
 
@@ -78,22 +81,31 @@
 With the addition of a Galaxy wrapper, developement moved here:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
 
-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)::
+
+    $ planemo shed_upload --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
+    ...
+
+or::
 
-    $ tar -czf align_back_trans.tar.gz tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml tools/align_back_trans/tool_dependencies.xml test-data/demo_nucs.fasta test-data/demo_nucs_trailing_stop.fasta test-data/demo_prot_align.fasta test-data/demo_nuc_align.fasta
+    $ planemo shed_upload --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
+    ...
+
+To just build and check the tar ball, use::
 
-Check this worked::
-
-    $ tar -tzf align_back_trans.tar.gz
+    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/align_back_trans/
+    ...
+    $ tar -tzf shed_upload.tar.gz 
+    test-data/demo_nucs.fasta
+    test-data/demo_nucs_trailing_stop.fasta
+    test-data/demo_prot_align.fasta
+    test-data/demo_nuc_align.fasta
     tools/align_back_trans/README.rst
     tools/align_back_trans/align_back_trans.py
     tools/align_back_trans/align_back_trans.xml
     tools/align_back_trans/tool_dependencies.xml
-    test-data/demo_nucs.fasta
-    test-data/demo_nucs_trailing_stop.fasta
-    test-data/demo_prot_align.fasta
-    test-data/demo_nuc_align.fasta
 
 
 Licence (MIT)
diff -r a7c7f10488f5 -r 174a38262fae tools/align_back_trans/align_back_trans.py
--- a/tools/align_back_trans/align_back_trans.py	Fri Nov 28 11:32:34 2014 -0500
+++ b/tools/align_back_trans/align_back_trans.py	Tue May 12 11:07:05 2015 -0400
@@ -29,7 +29,7 @@
     print "v0.0.5"
     sys.exit(0)
 
-def stop_err(msg, error_level=1):
+def sys_exit(msg, error_level=1):
     """Print error message to stdout and quit with given error level."""
     sys.stderr.write("%s\n" % msg)
     sys.exit(error_level)
@@ -37,7 +37,7 @@
 def check_trans(identifier, nuc, prot, table):
     """Returns nucleotide sequence if works (can remove trailing stop)"""
     if len(nuc) % 3:
-        stop_err("Nucleotide sequence for %s is length %i (not a multiple of three)"
+        sys_exit("Nucleotide sequence for %s is length %i (not a multiple of three)"
                  % (identifier, len(nuc)))
 
     p = str(prot).upper().replace("*", "X")
@@ -60,7 +60,7 @@
             err += "\nHowever, protein sequence found within translated nucleotides."
         elif p[1:] in t:
             err += "\nHowever, ignoring first amino acid, protein sequence found within translated nucleotides."
-        stop_err(err)
+        sys_exit(err)
 
 
     if t == p:
@@ -70,7 +70,7 @@
         if str(nuc[0:3]).upper() in ambiguous_generic_by_id[table].start_codons:
             return nuc
         else:
-            stop_err("Translation check failed for %s\n"
+            sys_exit("Translation check failed for %s\n"
                      "Would match if %s was a start codon (check correct table used)\n"
                      % (identifier, nuc[0:3].upper()))
     else:
@@ -85,7 +85,7 @@
                 sys.stderr.write("Protein:     %s\n" % p[offset:offset+60])
                 sys.stderr.write("             %s\n" % m[offset:offset+60])
                 sys.stderr.write("Translation: %s\n\n" % t[offset:offset+60])
-        stop_err("Translation check failed for %s\n" % identifier)
+        sys_exit("Translation check failed for %s\n" % identifier)
 
 def sequence_back_translate(aligned_protein_record, unaligned_nucleotide_record, gap, table=0):
     #TODO - Separate arguments for protein gap and nucleotide gap?
@@ -106,7 +106,7 @@
     if table:
         ungapped_nucleotide = check_trans(aligned_protein_record.id, ungapped_nucleotide, ungapped_protein, table)
     elif len(ungapped_protein) * 3 != len(ungapped_nucleotide):
-        stop_err("Inconsistent lengths for %s, ungapped protein %i, "
+        sys_exit("Inconsistent lengths for %s, ungapped protein %i, "
                  "tripled %i vs ungapped nucleotide %i" %
                  (aligned_protein_record.id,
                   len(ungapped_protein),
@@ -159,7 +159,7 @@
 elif len(sys.argv) == 6:
     align_format, prot_align_file, nuc_fasta_file, nuc_align_file, table = sys.argv[1:]
 else:
-    stop_err("""This is a Python script for 'back-translating' a protein alignment,
+    sys_exit("""This is a Python script for 'back-translating' a protein alignment,
 
 It requires three, four or five arguments:
 - alignment format (e.g. fasta, clustal),
@@ -184,7 +184,7 @@
 try:
     table = int(table)
 except:
-    stop_err("Bad table argument %r" % table)
+    sys_exit("Bad table argument %r" % table)
 
 prot_align = AlignIO.read(prot_align_file, align_format, alphabet=generic_protein)
 nuc_dict = SeqIO.index(nuc_fasta_file, "fasta")
diff -r a7c7f10488f5 -r 174a38262fae tools/align_back_trans/align_back_trans.xml
--- a/tools/align_back_trans/align_back_trans.xml	Fri Nov 28 11:32:34 2014 -0500
+++ b/tools/align_back_trans/align_back_trans.xml	Tue May 12 11:07:05 2015 -0400
@@ -1,18 +1,18 @@
-<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.5">
+<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.6">
     <description>Gives a codon aware alignment</description>
     <requirements>
         <requirement type="package" version="1.63">biopython</requirement>
         <requirement type="python-module">Bio</requirement>
     </requirements>
-    <version_command interpreter="python">align_back_trans.py --version</version_command>
-    <command interpreter="python">
-align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table"
-    </command>
     <stdio>
         <!-- Anything other than zero is an error -->
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command interpreter="python">align_back_trans.py --version</version_command>
+    <command interpreter="python">
+align_back_trans.py $prot_align.ext "$prot_align" "$nuc_file" "$out_nuc_align" "$table"
+    </command>
     <inputs>
         <param name="prot_align" type="data" format="fasta,muscle,clustal" label="Aligned protein file" help="Mutliple sequence file in FASTA, ClustalW or PHYLIP format." />
         <param name="table" type="select" label="Genetic code" help="Tables from the NCBI, these determine the start and stop codons">
@@ -38,7 +38,7 @@
         <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />
     </inputs>
     <outputs>
-        <data name="out_nuc_align" format="input" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/>
+        <data name="out_nuc_align" format_source="prot_align" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/>
     </outputs>
     <tests>
         <test>