# HG changeset patch
# User peterjc
# Date 1494431339 14400
# Node ID e5834d670ed8c5e07999652781fe4f5e3564d1dc
# Parent  61b4236e0cffc6fe68976b5cb4e5f566fa449a75
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans commit 7cf7d2e3fc5480fbe1a463e8a876e54c5c858dbe-dirty

diff -r 61b4236e0cff -r e5834d670ed8 tools/align_back_trans/README.rst
--- a/tools/align_back_trans/README.rst	Fri Apr 21 11:59:23 2017 -0400
+++ b/tools/align_back_trans/README.rst	Wed May 10 11:48:59 2017 -0400
@@ -72,6 +72,9 @@
 v0.0.7  - Minor Python code style improvements (internal change only).
 v0.0.8  - Python coding style change to avoid lamba (internal change only).
         - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
+        - Added recent NCBI genetic code tables:
+          *  Table 24. *Pterobranchia Mitochondrial Code*
+          *  Table 25. *Candidate Division SR1 and Gracilibacteria*
         - Use ``<command detect_errors="aggressive">`` (internal change only).
         - Single quote command line arguments (internal change only)
 ======= ======================================================================
diff -r 61b4236e0cff -r e5834d670ed8 tools/align_back_trans/align_back_trans.xml
--- a/tools/align_back_trans/align_back_trans.xml	Fri Apr 21 11:59:23 2017 -0400
+++ b/tools/align_back_trans/align_back_trans.xml	Wed May 10 11:48:59 2017 -0400
@@ -4,10 +4,10 @@
         <requirement type="package" version="1.67">biopython</requirement>
     </requirements>
     <version_command>
-python align_back_trans.py --version
+python $__tool_directory__/align_back_trans.py --version
 </version_command>
-    <command detect_errors="aggresive">
-align_back_trans.py $prot_align.ext '$prot_align' '$nuc_file' '$out_nuc_align' '$table'
+    <command detect_errors="aggressive">
+python $__tool_directory__/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." />
@@ -29,6 +29,16 @@
             <option value="21">21. Trematode Mitochondrial</option>
             <option value="22">22. Scenedesmus obliquus</option>
             <option value="23">23. Thraustochytrium Mitochondrial</option>
+            <option value="24">24. Pterobranchia Mitochondrial</option>
+            <option value="25">25. Candidate Division SR1 and Gracilibacteria</option>
+            <!-- TODO, these are not in Biopython 1.67
+            <option value="26">26. Pachysolen tannophilus Nuclear</option>
+            <option value="26">27. Karyorelict Nuclear</option>
+            <option value="26">28. Condylostoma Nuclear</option>
+            <option value="26">29. Mesodinium Nuclear</option>
+            <option value="26">30. Peritrich Nuclear</option>
+            <option value="26">31. Blastocrithidia Nuclear</option>
+            -->
             <option value="0">Don't check the translation</option>
         </param>
         <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" />