# HG changeset patch
# User iuc
# Date 1754081067 0
# Node ID 218f37ca06e420b3d4293c5de55970b13a146fc4

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep commit 21990794f87526caeb6e754d3f895da81d5f4a1f

diff -r 000000000000 -r 218f37ca06e4 eukrep.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/eukrep.xml	Fri Aug 01 20:44:27 2025 +0000
@@ -0,0 +1,149 @@
+<tool id="eukrep" name="EukRep" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0" license="MIT">
+    <description>Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.6.7</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">eukrep</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">eukrep</requirement>
+    </requirements>
+    <version_command>EukRep --version | cut -d" " -f 2</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    ln -s '$input' input.$input.ext &&
+    EukRep
+        -i input.$input.ext
+        -o 'output.fa'
+        ## -ff                   Force overwrite of existing output files
+        --min $min
+        ## --model MODEL         Path to an alternate trained linear SVM model. Default is lin_svm_160_3.0.pickle
+        --kmer_len $kmer_len
+        #if $prokarya
+            --prokarya 'output_prokarya.fa'
+        #end if
+        $seq_names
+        -m $stringency
+        --tie $tie
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz" label="Sequences"/>
+        <param argument="--min" type="integer" value="3000" min="0" label="Minimum sequence length cutoff" help="for sequences to be included in prediction"/>
+        <!--  -->
+        <param argument="--kmer_len" type="integer" value="5" min="3" max="6" label="K-mer length" help="K-mer length to use for making predictions"/>
+        <param argument="--prokarya" type="boolean" label="Output predicted prokaryotic sequences"/>
+        <param argument="--seq_names" type="boolean" truevalue="--seq_names" falsevalue="" label="Only output fasta headers" help="of identified sequences, instead of full FASTA entry"/>
+        <param name="stringency" argument="-m" type="select" label="Stringency" help="How stringent the algorithm is in identifying eukaryotic scaffolds. Strict has a lower false positive rate and true positive rate; vice verso for leneient">
+            <option value="strict">Strict</option>
+            <option value="balanced" selected="true">Balanced</option>
+            <option value="lenient">Lenient</option>
+        </param>
+        <param argument="--tie" type="select" label="Tie handling" help="Specify how to handle cases where an equal number of a sequences chunks are predicted to be of eukaryotic and prokaryotic origin (Generally occurs infrequently)">
+            <option value="euk" selected="true">Eukaryotic</option>
+            <option value="prok">Prokaryotic</option>
+            <option value="rand">Random</option>
+            <option value="skip">Do not classify</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" from_work_dir="output.fa" label="${tool.name} on ${on_string}">
+            <filter>not seq_names</filter>
+        </data>
+        <data name="output_prokarya" format="fasta" from_work_dir="output_prokarya.fa" label="${tool.name} on ${on_string}: Prokaryote sequences">
+            <filter>not seq_names</filter>
+            <filter>prokarya</filter>
+        </data>
+        <data name="output_names" format="txt" from_work_dir="output.fa" label="${tool.name} on ${on_string}: Eukaryote names">
+            <filter>seq_names</filter>
+        </data>
+        <data name="output_prokarya_names" format="txt" from_work_dir="output_prokarya.fa"  label="${tool.name} on ${on_string}: Prokaryote names">
+            <filter>prokarya</filter>
+            <filter>seq_names</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="test_scaffolds.fa" location="https://github.com/patrickwest/EukRep/raw/refs/tags/v0.6.6/tests/test_sequences/test_scaffolds.fa"/>
+            <param name="kmer_len" value="4"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line=">test_sequence_5" n="1"/>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="test_scaffolds.fa" location="https://github.com/patrickwest/EukRep/raw/refs/tags/v0.6.6/tests/test_sequences/test_scaffolds.fa"/>
+            <param name="kmer_len" value="4"/>
+            <param name="seq_names" value="true"/>
+            <output name="output_names">
+                <assert_contents>
+                    <has_line line="test_sequence_5" n="1"/>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input" value="test_scaffolds.fa" location="https://github.com/patrickwest/EukRep/raw/refs/tags/v0.6.6/tests/test_sequences/test_scaffolds.fa"/>
+            <param name="kmer_len" value="4"/>
+            <param name="prokarya" value="true"/>
+            <output name="output">
+                <assert_contents>
+                    <has_line line=">test_sequence_5" n="1"/>
+                    <has_n_lines n="2"/>
+                </assert_contents>
+            </output>
+            <output name="output_prokarya">
+                <assert_contents>
+                    <has_line line=">test_sequence_5" negate="true"/>
+                    <has_n_lines n="24"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input" value="test_scaffolds.fa" location="https://github.com/patrickwest/EukRep/raw/refs/tags/v0.6.6/tests/test_sequences/test_scaffolds.fa"/>
+            <param name="kmer_len" value="4"/>
+            <param name="seq_names" value="true"/>
+            <param name="prokarya" value="true"/>
+            <output name="output_names">
+                <assert_contents>
+                    <has_line line="test_sequence_5" n="1"/>
+                    <has_n_lines n="1"/>
+                </assert_contents>
+            </output>
+            <output name="output_prokarya_names">
+                <assert_contents>
+                    <has_line line="test_sequence_5" negate="true"/>
+                    <has_n_lines n="12"/>
+                </assert_contents>
+            </output>
+
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasetsocs/ref/rst/restructuredtext.html)
+
+Usage
+.....
+
+
+**Input**
+
+Sequences in FASTA format.
+
+**Output**
+
+Eukaryotic sequences in FASTA format.
+
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1101/gr.228429.117</citation>
+    </citations>
+</tool>
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