diff tools/align_back_trans/align_back_trans.xml @ 4:c8469274d136 draft

v0.0.8 Using Biopython 1.67 from Tool Shed or Conda package

--- a/tools/align_back_trans/align_back_trans.xml	Wed Feb 01 06:55:27 2017 -0500
+++ b/tools/align_back_trans/align_back_trans.xml	Wed May 10 12:05:28 2017 -0400
@@ -1,17 +1,13 @@
-<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.7">
+<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.8">
     <description>Gives a codon aware alignment</description>
     <requirements>
-        <requirement type="package" version="1.63">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
+        <requirement type="package" version="1.67">biopython</requirement>
     </requirements>
-    <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"
+    <version_command>
+python $__tool_directory__/align_back_trans.py --version
+</version_command>
+    <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." />
@@ -33,6 +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" />