Mercurial > repos > iuc > eukrep
changeset 0:218f37ca06e4 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep commit 21990794f87526caeb6e754d3f895da81d5f4a1f
| author | iuc |
|---|---|
| date | Fri, 01 Aug 2025 20:44:27 +0000 |
| parents | |
| children | |
| files | eukrep.xml |
| diffstat | 1 files changed, 149 insertions(+), 0 deletions(-) [+] |
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--- /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> \ No newline at end of file