Added mirmachine optional arguments (#5913)

* Added mirmachine optional arguments * Add missing end character * Added boolean arguments * Try different parameter name hyphens becoming underscores with planemo * need to bump --------- Co-authored-by: Björn Grüning <[email protected]>
galaxyproject · Mar 27, 2024 · 305061c · 305061c
1 parent d3d2bb5
commit 305061c
Show file tree

Hide file tree

Showing 2 changed files with 63 additions and 1 deletion.
diff --git 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>
@@ -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
@@ -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"/>