mitos2: add missing genetic codes (galaxyproject#5968)

* mitos2: add missing genetic codes https://help.galaxyproject.org/t/mitos-2-yeast-genetic-code/12281/2 * bump mitos * fix mitos2 test data phase for protein coding genes is now always 0
bebatut · May 2, 2024 · 921fa90 · 921fa90
1 parent 162c595
commit 921fa90
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/tools/mitos/mitos.xml b/tools/mitos/mitos.xml
@@ -3,7 +3,7 @@
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS</token>
-    <token name="@TOOL_VERSION@">1.1.6</token>
+    <token name="@TOOL_VERSION@">1.1.7</token>
     <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <xrefs>

diff --git a/tools/mitos/mitos2.xml b/tools/mitos/mitos2.xml
@@ -3,7 +3,7 @@
   <macros>
     <import>macros.xml</import>
     <token name="@MITOS_NAME@">MITOS2</token>
-    <token name="@TOOL_VERSION@">2.1.8</token>
+    <token name="@TOOL_VERSION@">2.1.9</token>
     <token name="@VERSION_SUFFIX@">0</token>
   </macros>
   <xrefs>
@@ -64,11 +64,15 @@ $advanced_ncrna.sensitive
     </param> 
     <param argument="--code" label="Genetic code" type="select">
       <option value="2">Vertebrate (2)</option>
+      <option value="3">Yeast (3)</option>
       <option value="4">Mold, Protozoan, Coelenteral (4)</option>
       <option value="5">Invertebrate (5)</option>
       <option value="9">Echinoderm, Flatworm (9)</option>
       <option value="13">Ascidian (13)</option>
       <option value="14">Alternative Flatworm (14)</option>
+      <option value="21">Trematode (21)</option>
+      <option value="24">Rhabdopleuridae (24)</option>
+      <option value="33">Cephalodiscidae (33)</option>
     </param>
     <param argument="--refseqver" label="Reference data" type="select" help="Contact the administrator of this Galaxy instance if you miss reference data">
         <options from_data_table="mitos">

diff --git a/tools/mitos/test-data/mitos2_NC_012920.gff b/tools/mitos/test-data/mitos2_NC_012920.gff
@@ -44,7 +44,7 @@ NC_012920\tmitfi\tncRNA_gene\t12266\t12336\t\.\t\+\t\.\tID=gene_trnL1;Name=trnL1
 NC_012920\tmitfi\ttRNA\t12266\t12336\t\.\t\+\t\.\tID=transcript_trnL1\(tag\);Name=trnL1\(tag\);Parent=gene_trnL1\(tag\);gene_id=trnL1\(tag\)
 NC_012920\tmitfi\texon\t12266\t12336\t0\.026000000536441803\t\+\t\.\tParent=transcript_trnL1;Name=trnL1
 NC_012920\tmitos\tgene\t14149\t14670\t\.\t-\t\.\tID=gene_nad6;Name=nad6;gene_id=nad6
-NC_012920\tmitos\texon\t14149\t14670\t39\.7\t-\t2\.0\tParent=transcript_nad6;Name=nad6
+NC_012920\tmitos\texon\t14149\t14670\t39\.7\t-\t0\tParent=transcript_nad6;Name=nad6
 NC_012920\tmitfi\tncRNA_gene\t14674\t14742\t\.\t-\t\.\tID=gene_trnE;Name=trnE;gene_id=trnE
 NC_012920\tmitfi\ttRNA\t14674\t14742\t\.\t-\t\.\tID=transcript_trnE\(ttc\);Name=trnE\(ttc\);Parent=gene_trnE\(ttc\);gene_id=trnE\(ttc\)
 NC_012920\tmitfi\texon\t14674\t14742\t0\.03200000151991844\t-\t\.\tParent=transcript_trnE;Name=trnE