# HG changeset patch
# User iuc
# Date 1711527543 0
# Node ID 85010d0eaa6cce633f705ef00c09aa600741057b
# Parent  f2e87c81497d789d3083d8f99d41dbc7e5d30efa
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mirmachine commit 305061c25b6fcf54d960f17c2cad15c30fb2e26a

diff -r f2e87c81497d -r 85010d0eaa6c macros.xml
--- a/macros.xml	Fri Mar 15 16:16:00 2024 +0000
+++ b/macros.xml	Wed Mar 27 08:19:03 2024 +0000
@@ -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>
@@ -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 -r f2e87c81497d -r 85010d0eaa6c mirmachine.xml
--- a/mirmachine.xml	Fri Mar 15 16:16:00 2024 +0000
+++ b/mirmachine.xml	Wed Mar 27 08:19:03 2024 +0000
@@ -9,6 +9,9 @@
     MirMachine.py
         -n '$input_node'
         -s '$input_species'
+        -m '$model'
+        $a
+        $o
         --genome ./genome.fasta
         -c \${GALAXY_SLOTS:-8}
     &&
@@ -29,6 +32,11 @@
             </sanitizer>
             <validator type="regex">[a-zA-Z_]+</validator>
         </param>
+        <param type="select" name="model" label="Model" help="Model type: deutero, proto, combined">
+            <expand macro="model_options"/>
+        </param>
+        <param type="boolean" optional="true" truevalue="-a" falsevalue="" argument="-a" label="Add all nodes" help="Move on the tree both ways"/>
+        <param type="boolean" optional="true" truevalue="-o" falsevalue="" argument="-o" label="Single node only" help="Run only on the given node for miRNA families"/>
     </inputs>
     <outputs>
         <data name="gff_file" format="gff" from_work_dir="species.PRE.gff" label="${tool.name} on ${on_string}: GFF file"/>
@@ -56,11 +64,60 @@
                 </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="a" 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="o" 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"/>