From b23d3e203075027ae9b2eb28d69d608a1ff20565 Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Tue, 26 Mar 2024 16:10:01 +0100
Subject: [PATCH 1/5] Added mirmachine optional arguments

---
 tools/mirmachine/macros.xml     |  5 +++
 tools/mirmachine/mirmachine.xml | 55 +++++++++++++++++++++++++++++++++
 2 files changed, 60 insertions(+)

diff --git a/tools/mirmachine/macros.xml b/tools/mirmachine/macros.xml
index d0b84d9721c..e1fa38263cd 100644
--- a/tools/mirmachine/macros.xml
+++ b/tools/mirmachine/macros.xml
@@ -24,6 +24,11 @@
             <citation type="doi">10.1016/j.xgen.2023.100348</citation>
         </citations>
     </xml>
+    <xml name="model_options">
+        <option value="deutero">deutero</option>
+        <option value="proto">proto</option>
+        <option value="combined" selected="true">combined</option>
+    </xml>
     <xml name="node_options">
         <option value="Acanthomorpha">Acanthomorpha</option>
         <option value="Ambulacraria">Ambulacraria</option>
diff --git a/tools/mirmachine/mirmachine.xml b/tools/mirmachine/mirmachine.xml
index 9fc6bb14bf9..32d4e39de2c 100644
--- a/tools/mirmachine/mirmachine.xml
+++ b/tools/mirmachine/mirmachine.xml
@@ -9,6 +9,7 @@
     MirMachine.py
         -n '$input_node'
         -s '$input_species'
+        -m '$model'
         --genome ./genome.fasta
         -c \${GALAXY_SLOTS:-8}
     &&
@@ -29,6 +30,11 @@
             </sanitizer>
             <validator type="regex">[a-zA-Z_]+</validator>
         </param>
+        <param type="select" name="model" label="Model" help="Model type: deutero, proto, combined">
+            <expand macro="model_options">
+        </param>
+        <param type="boolean" optional="true" truevalue="--add-all-nodes" falsevalue="" argument="--add-all-nodes" label="Add all nodes" help="Move on the tree both ways"/>
+        <param type="boolean" optional="true" truevalue="--single-node-only" falsevalue="" argument="--single-node-only" label="Single node only" help="Run only on the given node for miRNA families"/>
     </inputs>
     <outputs>
         <data name="gff_file" format="gff" from_work_dir="species.PRE.gff" label="${tool.name} on ${on_string}: GFF file"/>
@@ -56,11 +62,60 @@
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="3">
+            <param name="genome" value="ref.fa"/>
+            <param name="input_node" value="Caenorhabditis"/>
+            <param name="input_species" value="Caenorhabditis_elegans"/>
+            <param name="add-all-nodes" value="true"/>
+            <output name="gff_file">
+                <assert_contents>
+                    <has_n_lines n="24" delta="0"/>
+                </assert_contents>
+            </output>
+            <output name="filtered_gff_file">
+                <assert_contents>
+                    <has_n_lines n="15" delta="0"/>
+                </assert_contents>
+            </output>
+            <output name="fasta_file">
+                <assert_contents>
+                    <has_n_lines n="24" delta="0"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="3">
+            <param name="genome" value="ref.fa"/>
+            <param name="input_node" value="Caenorhabditis"/>
+            <param name="input_species" value="Caenorhabditis_elegans"/>
+            <param name="single-node-only" value="true"/>
+            <output name="gff_file">
+                <assert_contents>
+                    <has_n_lines n="19" delta="0"/>
+                </assert_contents>
+            </output>
+            <output name="filtered_gff_file">
+                <assert_contents>
+                    <has_n_lines n="12" delta="0"/>
+                </assert_contents>
+            </output>
+            <output name="fasta_file">
+                <assert_contents>
+                    <has_n_lines n="14" delta="0"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help><![CDATA[
 
 Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements. MirMachine facilitates automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.
 
+The MirMachine main executable will generate GFF annotations (filtered and unfiltered) and some other files
+
+`gff` All predicted miRNA families
+`filtered_gff` High confidence miRNA family predictions after bitscore filtering. (This file is what you need in most cases)
+`fasta` Both high and low confidence predictions in FASTA format
+
+miRNA prediction score is given in the header of the output filtered gff file
     ]]></help>
     <expand macro="citations"/>
     <expand macro="creator"/>

From 9749c9e1cc224c9621ef208a8017dfa177efe48c Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Tue, 26 Mar 2024 16:16:44 +0100
Subject: [PATCH 2/5] Add missing end character

---
 tools/mirmachine/mirmachine.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mirmachine/mirmachine.xml b/tools/mirmachine/mirmachine.xml
index 32d4e39de2c..bf43896d982 100644
--- a/tools/mirmachine/mirmachine.xml
+++ b/tools/mirmachine/mirmachine.xml
@@ -31,7 +31,7 @@
             <validator type="regex">[a-zA-Z_]+</validator>
         </param>
         <param type="select" name="model" label="Model" help="Model type: deutero, proto, combined">
-            <expand macro="model_options">
+            <expand macro="model_options"/>
         </param>
         <param type="boolean" optional="true" truevalue="--add-all-nodes" falsevalue="" argument="--add-all-nodes" label="Add all nodes" help="Move on the tree both ways"/>
         <param type="boolean" optional="true" truevalue="--single-node-only" falsevalue="" argument="--single-node-only" label="Single node only" help="Run only on the given node for miRNA families"/>

From ad1bc05f90673fedafa728109ed75ec91f2c9694 Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Tue, 26 Mar 2024 16:32:12 +0100
Subject: [PATCH 3/5] Added boolean arguments

---
 tools/mirmachine/mirmachine.xml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tools/mirmachine/mirmachine.xml b/tools/mirmachine/mirmachine.xml
index bf43896d982..af35a979725 100644
--- a/tools/mirmachine/mirmachine.xml
+++ b/tools/mirmachine/mirmachine.xml
@@ -10,6 +10,8 @@
         -n '$input_node'
         -s '$input_species'
         -m '$model'
+        $add-all-nodes
+        $single-node-only
         --genome ./genome.fasta
         -c \${GALAXY_SLOTS:-8}
     &&

From 9f14b7eb0ba9ed6cf53888c8f29c4e9424e016a7 Mon Sep 17 00:00:00 2001
From: tbrown91 <brown@izw-berlin.de>
Date: Tue, 26 Mar 2024 16:46:39 +0100
Subject: [PATCH 4/5] Try different parameter name hyphens becoming underscores
 with planemo

---
 tools/mirmachine/mirmachine.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/tools/mirmachine/mirmachine.xml b/tools/mirmachine/mirmachine.xml
index af35a979725..d517c8b282d 100644
--- a/tools/mirmachine/mirmachine.xml
+++ b/tools/mirmachine/mirmachine.xml
@@ -10,8 +10,8 @@
         -n '$input_node'
         -s '$input_species'
         -m '$model'
-        $add-all-nodes
-        $single-node-only
+        $a
+        $o
         --genome ./genome.fasta
         -c \${GALAXY_SLOTS:-8}
     &&
@@ -35,8 +35,8 @@
         <param type="select" name="model" label="Model" help="Model type: deutero, proto, combined">
             <expand macro="model_options"/>
         </param>
-        <param type="boolean" optional="true" truevalue="--add-all-nodes" falsevalue="" argument="--add-all-nodes" label="Add all nodes" help="Move on the tree both ways"/>
-        <param type="boolean" optional="true" truevalue="--single-node-only" falsevalue="" argument="--single-node-only" label="Single node only" help="Run only on the given node for miRNA families"/>
+        <param type="boolean" optional="true" truevalue="-a" falsevalue="" argument="-a" label="Add all nodes" help="Move on the tree both ways"/>
+        <param type="boolean" optional="true" truevalue="-o" falsevalue="" argument="-o" label="Single node only" help="Run only on the given node for miRNA families"/>
     </inputs>
     <outputs>
         <data name="gff_file" format="gff" from_work_dir="species.PRE.gff" label="${tool.name} on ${on_string}: GFF file"/>
@@ -68,7 +68,7 @@
             <param name="genome" value="ref.fa"/>
             <param name="input_node" value="Caenorhabditis"/>
             <param name="input_species" value="Caenorhabditis_elegans"/>
-            <param name="add-all-nodes" value="true"/>
+            <param name="a" value="true"/>
             <output name="gff_file">
                 <assert_contents>
                     <has_n_lines n="24" delta="0"/>
@@ -89,7 +89,7 @@
             <param name="genome" value="ref.fa"/>
             <param name="input_node" value="Caenorhabditis"/>
             <param name="input_species" value="Caenorhabditis_elegans"/>
-            <param name="single-node-only" value="true"/>
+            <param name="o" value="true"/>
             <output name="gff_file">
                 <assert_contents>
                     <has_n_lines n="19" delta="0"/>

From 8139c382427c546f74b8f6c4590b08dff0f8fb3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= <bjoern@gruenings.eu>
Date: Tue, 26 Mar 2024 22:35:13 +0100
Subject: [PATCH 5/5] need to bump

---
 tools/mirmachine/macros.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/mirmachine/macros.xml b/tools/mirmachine/macros.xml
index e1fa38263cd..8b0506e7275 100644
--- a/tools/mirmachine/macros.xml
+++ b/tools/mirmachine/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.2.13</token>
-    <token name="@SUFFIX_VERSION@">0</token>
+    <token name="@SUFFIX_VERSION@">1</token>
     <xml name="edam_ontology">
         <edam_topics>
             <edam_topic>topic_0659</edam_topic>