From 9419bd6d65199967c2b265f9fc222edabf1a9b19 Mon Sep 17 00:00:00 2001
From: rlibouban <romane.libouban@irisa.fr>
Date: Thu, 28 Mar 2024 16:32:20 +0100
Subject: [PATCH 1/4] update version

---
 tools/miniprot/macros.xml   |  3 ++-
 tools/miniprot/miniprot.xml | 23 +++++++++++++++++------
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/tools/miniprot/macros.xml b/tools/miniprot/macros.xml
index 0ee0edde121..145ed88d7c6 100644
--- a/tools/miniprot/macros.xml
+++ b/tools/miniprot/macros.xml
@@ -1,5 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.12</token>
+    <token name="@TOOL_VERSION@">0.13</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="citation">
         <citations>
             <citation type="doi">10.1093/bioinformatics/btad014</citation> 
diff --git a/tools/miniprot/miniprot.xml b/tools/miniprot/miniprot.xml
index a01534aea92..a5e396e15f6 100644
--- a/tools/miniprot/miniprot.xml
+++ b/tools/miniprot/miniprot.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy0" profile="21.05">
+<tool id="miniprot" name="Miniprot align" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>align a protein sequence against a genome with affine gap penalty, splicing and frameshift</description>
     <macros>
         <import>macros.xml</import>
@@ -25,7 +25,10 @@
             -C $adv.alignment.non_canonical_splice
             -F $adv.alignment.frameshift
             -B $adv.alignment.end_bonus
-            -j $adv.alignment.splice_model 
+            -j $adv.alignment.splice_model
+            #if str($adv.ncbi_table) !=""
+                -T '$adv.ncbi_table' 
+            #end if
         #if str($adv.mapping.intron_size.mode) == 'manual'
             -G $adv.mapping.intron_size.max_intron      
         #elif str($adv.mapping.intron_size.mode) == 'auto'
@@ -71,7 +74,7 @@
                 <param argument="-k" name="kmer_size" type="integer" min="1" value="6" label="K-mer size for genome-wide indexing"/>
                 <param argument="-b" name="bits_per_block" type="integer" min="1" value="8" label="Number of bits per bin" help="Miniprot splits the genome into non-overlapping bins of 2^8 bp in size"/>
                 <param argument="-M" name="modimisers" type="integer" value="1" label="Sample k-mers at a rate 1/2**INT" help="Increasing this option reduces peak memory but decreases sensitivity"/>
-                <param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index"/>           
+                <param argument="-L" name="min_ORF" type="integer" value="30" label="Minimum ORF length to index"/>
             </when>
             <when value="preindexed">
                 <!-- refine the datatype here once Miniprot index data type is in Galaxy -->
@@ -142,10 +145,17 @@
                     <param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/>
                 </section>
                 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
+                <param argument="-T" name="ncbi_table" type="text" optional="true" label="Enter NCBI translation table" help="1 through 33 except 7-8 and 17-20">
+                    <sanitizer invalid_char="">
+                        <valid initial="string.digits"></valid>
+                    </sanitizer>
+                    <validator type="regex">[0-9]+</validator>
+                </param>           
             </when>
             <when value="no">
             </when>
         </conditional>
+
     </inputs>
     <outputs>
         <data name="output_alignment" format="gff3" label="Miniprot on ${on_string}">
@@ -235,7 +245,7 @@
                 <assert_contents>
                     <has_text text="tr|I6YGH7|I6YGH7_MYCTU" />
                     <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
-                    <has_n_lines n="1633"/>
+                    <has_n_lines n="1647"/>
                 </assert_contents>
             </output>
         </test>
@@ -257,7 +267,7 @@
                     <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
                     <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
                     <has_text text="NC_000962.3"/>
-                    <has_n_lines n="2172"/>
+                    <has_n_lines n="2196"/>
                 </assert_contents>
             </output>
         </test>
@@ -279,7 +289,7 @@
                     <has_text text="tr|I6YGH7|I6YGH7_MYCTU"/>
                     <has_text text="VDIDLDPSTEKLRAQIRAEVAALKAMPREPRTVAIAEGGWVLPYLPKPWGRAASPVEQIIIAQEFTAGRVKRPQIAIATWIVPSIVAFGTDNQKQRLLPPTFRGDIFWCQLFSEPGAGSDLASLATKATRVDGGWRITGQKIWTTGAQYSQWGALLARTDPSAPKHNGITYFLLDMKSEGVQVKPLRELTGKEFFNTVYLDDVFVPDELVLGEVNRGWEVSRNTLTAERVSIGGSDSTFLPTLGEFVDFVRDYRFEGQFDQVARHRAGQLIAEGHATKLLNLRSTLLTLAGGDPMAPAAISKLLSMRTGQGYAEFAVSSFGTDAVIGDTERLPGKWGEYLLASRATTIYGGTSEVQLNIIAERLLGLPRDP"/>
                     <has_text text="sp|O05779|FTSE_MYCTU"/>
-                    <has_n_lines n="650"/>
+                    <has_n_lines n="654"/>
                 </assert_contents>
             </output>
         </test>
@@ -332,6 +342,7 @@
             </conditional>
             <param name="protein_fasta" value="input_query.fasta.gz" ftype="fasta"></param>
             <param name="output_format" value="gtf"></param>
+            <param name="ncbi_table" value="1"></param>
             <conditional name="adv">
                 <param name="options" value="yes"></param>
                 <section name="output">

From 8b58b5377ca3870157f538f28348cf3c6ecf7b34 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 28 Mar 2024 17:06:02 +0100
Subject: [PATCH 2/4] Update tools/miniprot/miniprot.xml

---
 tools/miniprot/miniprot.xml | 34 ++++++++++++++++++++++++++++------
 1 file changed, 28 insertions(+), 6 deletions(-)

diff --git a/tools/miniprot/miniprot.xml b/tools/miniprot/miniprot.xml
index a5e396e15f6..0c87039e678 100644
--- a/tools/miniprot/miniprot.xml
+++ b/tools/miniprot/miniprot.xml
@@ -145,12 +145,34 @@
                     <param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/>
                 </section>
                 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
-                <param argument="-T" name="ncbi_table" type="text" optional="true" label="Enter NCBI translation table" help="1 through 33 except 7-8 and 17-20">
-                    <sanitizer invalid_char="">
-                        <valid initial="string.digits"></valid>
-                    </sanitizer>
-                    <validator type="regex">[0-9]+</validator>
-                </param>           
+              <param argument="-T" name="ncbi_table" type="select" optional="true" label="Enter NCBI translation table">
+                  <option value="1">1 Standard</option>
+                  <option value="1">1 Standard code</option>
+                  <option value="2">2 Vertebrate mitochondrial</option>
+                  <option value="3">3 Yeast mitochondrial</option>
+                  <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option>
+                  <option value="5">5 Invertebrate mitochondrial</option>
+                  <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option>
+                  <option value="9">9 Echinoderm and flatworm mitochondrial</option>
+                  <option value="10">10 Euplotid nuclear</option>
+                  <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option>
+                  <option value="12">12 Alternative yeast nuclear</option>
+                  <option value="13">13 Ascidian mitochondrial</option>
+                  <option value="14">14 Alternative flatworm mitochondrial</option>
+                  <option value="16">16 Chlorophycean mitochondrial</option>
+                  <option value="21">21 Trematode Mitochondrial</option>
+                  <option value="22">22 Scenedesmus obliquus Mitochondrial</option>
+                  <option value="23">23 Thraustochytrium Mitochondrial</option>
+                  <option value="24">24 Rhabdopleuridae Mitochondrial</option>
+                  <option value="25">25 Candidate Division SR1 and Gracilibacteria</option>
+                  <option value="26">26 Pachysolen tannophilus Nuclear</option>
+                  <option value="27">27 Karyorelict Nuclear</option>
+                  <option value="28">28 Condylostoma Nuclear</option>
+                  <option value="29">29 Mesodinium nuclear</option>
+                  <option value="30">30 Peritrich nuclear</option>
+                  <option value="31">31 Blastocrithidia nuclear</option>
+                  <option value="33">33 Cephalodiscidae mitochondrial</option>
+            </param>
             </when>
             <when value="no">
             </when>

From 34fbc874c1e7c9029758fb26ce8a91b78b11a5f1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 28 Mar 2024 17:07:34 +0100
Subject: [PATCH 3/4] fix spacing

---
 tools/miniprot/miniprot.xml | 58 ++++++++++++++++++-------------------
 1 file changed, 29 insertions(+), 29 deletions(-)

diff --git a/tools/miniprot/miniprot.xml b/tools/miniprot/miniprot.xml
index 0c87039e678..021a30adc15 100644
--- a/tools/miniprot/miniprot.xml
+++ b/tools/miniprot/miniprot.xml
@@ -145,34 +145,34 @@
                     <param argument="--no-cs" name="output_no_cs" type="boolean" truevalue="--no-cs" falsevalue="" checked="false" label="Disable the cs tag"/>
                 </section>
                 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
-              <param argument="-T" name="ncbi_table" type="select" optional="true" label="Enter NCBI translation table">
-                  <option value="1">1 Standard</option>
-                  <option value="1">1 Standard code</option>
-                  <option value="2">2 Vertebrate mitochondrial</option>
-                  <option value="3">3 Yeast mitochondrial</option>
-                  <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option>
-                  <option value="5">5 Invertebrate mitochondrial</option>
-                  <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option>
-                  <option value="9">9 Echinoderm and flatworm mitochondrial</option>
-                  <option value="10">10 Euplotid nuclear</option>
-                  <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option>
-                  <option value="12">12 Alternative yeast nuclear</option>
-                  <option value="13">13 Ascidian mitochondrial</option>
-                  <option value="14">14 Alternative flatworm mitochondrial</option>
-                  <option value="16">16 Chlorophycean mitochondrial</option>
-                  <option value="21">21 Trematode Mitochondrial</option>
-                  <option value="22">22 Scenedesmus obliquus Mitochondrial</option>
-                  <option value="23">23 Thraustochytrium Mitochondrial</option>
-                  <option value="24">24 Rhabdopleuridae Mitochondrial</option>
-                  <option value="25">25 Candidate Division SR1 and Gracilibacteria</option>
-                  <option value="26">26 Pachysolen tannophilus Nuclear</option>
-                  <option value="27">27 Karyorelict Nuclear</option>
-                  <option value="28">28 Condylostoma Nuclear</option>
-                  <option value="29">29 Mesodinium nuclear</option>
-                  <option value="30">30 Peritrich nuclear</option>
-                  <option value="31">31 Blastocrithidia nuclear</option>
-                  <option value="33">33 Cephalodiscidae mitochondrial</option>
-            </param>
+                <param argument="-T" name="ncbi_table" type="select" optional="true" label="Enter NCBI translation table">
+                    <option value="1">1 Standard</option>
+                    <option value="1">1 Standard code</option>
+                    <option value="2">2 Vertebrate mitochondrial</option>
+                    <option value="3">3 Yeast mitochondrial</option>
+                    <option value="4">4 Mold, Protozoan, and Coelenterate Mitochondrial and the Mycoplasma/Spiroplasma</option>
+                    <option value="5">5 Invertebrate mitochondrial</option>
+                    <option value="6">6 Ciliate, dasycladacean and hexamita nuclear</option>
+                    <option value="9">9 Echinoderm and flatworm mitochondrial</option>
+                    <option value="10">10 Euplotid nuclear</option>
+                    <option value="11" selected="true">11 Bacterial, Archaeal and Plant Plastid</option>
+                    <option value="12">12 Alternative yeast nuclear</option>
+                    <option value="13">13 Ascidian mitochondrial</option>
+                    <option value="14">14 Alternative flatworm mitochondrial</option>
+                    <option value="16">16 Chlorophycean mitochondrial</option>
+                    <option value="21">21 Trematode Mitochondrial</option>
+                    <option value="22">22 Scenedesmus obliquus Mitochondrial</option>
+                    <option value="23">23 Thraustochytrium Mitochondrial</option>
+                    <option value="24">24 Rhabdopleuridae Mitochondrial</option>
+                    <option value="25">25 Candidate Division SR1 and Gracilibacteria</option>
+                    <option value="26">26 Pachysolen tannophilus Nuclear</option>
+                    <option value="27">27 Karyorelict Nuclear</option>
+                    <option value="28">28 Condylostoma Nuclear</option>
+                    <option value="29">29 Mesodinium nuclear</option>
+                    <option value="30">30 Peritrich nuclear</option>
+                    <option value="31">31 Blastocrithidia nuclear</option>
+                    <option value="33">33 Cephalodiscidae mitochondrial</option>
+                </param>
             </when>
             <when value="no">
             </when>
@@ -393,4 +393,4 @@
         .. _overview: https://github.com/lh3/miniprot#algorithm-overview
     ]]></help> 
     <expand macro="citation"></expand>
-</tool>
\ No newline at end of file
+</tool>

From 605c2f2188ff02de0b0178bf8a0f587857fa11fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Thu, 28 Mar 2024 18:02:58 +0100
Subject: [PATCH 4/4] Update miniprot.xml

---
 tools/miniprot/miniprot.xml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tools/miniprot/miniprot.xml b/tools/miniprot/miniprot.xml
index 021a30adc15..0f60cb80e24 100644
--- a/tools/miniprot/miniprot.xml
+++ b/tools/miniprot/miniprot.xml
@@ -146,7 +146,6 @@
                 </section>
                 <param argument="-K" name="query_batch_size" type="integer" min="1" value="2000000" label="Query batch size"/>
                 <param argument="-T" name="ncbi_table" type="select" optional="true" label="Enter NCBI translation table">
-                    <option value="1">1 Standard</option>
                     <option value="1">1 Standard code</option>
                     <option value="2">2 Vertebrate mitochondrial</option>
                     <option value="3">3 Yeast mitochondrial</option>