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Added mirmachine optional arguments #5913

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merged 5 commits into from
Mar 27, 2024
Merged

Added mirmachine optional arguments #5913

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b23d3e2
Added mirmachine optional arguments
tbrown91 Mar 26, 2024
9749c9e
Add missing end character
tbrown91 Mar 26, 2024
ad1bc05
Added boolean arguments
tbrown91 Mar 26, 2024
9f14b7e
Try different parameter name hyphens becoming underscores with planemo
tbrown91 Mar 26, 2024
8139c38
need to bump
bgruening Mar 26, 2024
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5 changes: 5 additions & 0 deletions tools/mirmachine/macros.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -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>
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57 changes: 57 additions & 0 deletions tools/mirmachine/mirmachine.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,9 @@
MirMachine.py
-n '$input_node'
-s '$input_species'
-m '$model'
$a
$o
--genome ./genome.fasta
-c \${GALAXY_SLOTS:-8}
&&
Expand All @@ -29,6 +32,11 @@
</sanitizer>
<validator type="regex">[a-zA-Z_]+</validator>
</param>
<param type="select" name="model" label="Model" help="Model type: deutero, proto, combined">
<expand macro="model_options"/>
</param>
<param type="boolean" optional="true" truevalue="-a" falsevalue="" argument="-a" label="Add all nodes" help="Move on the tree both ways"/>
<param type="boolean" optional="true" truevalue="-o" falsevalue="" argument="-o" label="Single node only" help="Run only on the given node for miRNA families"/>
</inputs>
<outputs>
<data name="gff_file" format="gff" from_work_dir="species.PRE.gff" label="${tool.name} on ${on_string}: GFF file"/>
Expand Down Expand Up @@ -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"/>
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