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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig commit 8d5424b11bc4d5a4112b030dc38016e4d8b60e21
author | iuc |
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date | Tue, 23 May 2023 17:04:29 +0000 |
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<?xml version="1.0"?> <tool id="deepsig" name="DeepSig" version="@TOOL_VERSION@+galaxy0" profile="21.05"> <description>signal peptides predictor</description> <macros> <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">deepsig</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ deepsig -f '$input_fasta' -o '$output' -k $organism -m $output_format -t \${GALAXY_SLOTS:-1} ]]></command> <inputs> <param name="input_fasta" argument="-f" type="data" format="fasta" label="Protein sequences"/> <param name="organism" argument="-k" type="select" label="Taxonomic domain"> <option value="euk" selected="true">Eukaryotes</option> <option value="gramp">Gram-positive</option> <option value="gramn">Gram-negative</option> </param> <param name="output_format" argument="-m" type="select" label="output_format"> <option value="gff3" selected="true">GFF3</option> <option value="json">JSON</option> </param> </inputs> <outputs> <data name="output" format="gff3" label="DeepSig on ${on_string}"> <change_format> <when input="output_format" value="json" format="json"/> </change_format> </data> </outputs> <tests> <test expect_num_outputs="1"> <param name="input_fasta" value="G5ED35.fasta"/> <param name="organism" value="euk"/> <param name="output_format" value="gff3"/> <output name="output" ftype="gff3"> <assert_contents> <has_text text="sp|G5ED35|TTR52_CAEEL"/> <has_text text="evidence=ECO:0000256"/> </assert_contents> </output> </test> <test expect_num_outputs="1"> <param name="input_fasta" value="G5ED35.fasta"/> <param name="organism" value="euk"/> <param name="output_format" value="json"/> <output name="output" ftype="json"> <assert_contents> <has_text text='"sequence": "MSRFLIYFLPFFIYSGNVLSKTSCLMATGVLKCPTDPEAVKKVHIDLWDEDSLPLESDDLMGRTWSDRNGNFQVTGCASDFGPINTPDPYLYIQHNCPHRDSNATNPIQIDVIPLFLPSIVRLGNVYLDRYLEDY"'/> </assert_contents> </output> </test> </tests> <help><![CDATA[ deepsig_ Predictor of signal peptides in proteins based on deep learning. DeepSig is a novel approach to predict signal peptides in proteins based on deep learning and sequence labelling methods. The proposed approach was evaluated and compared with other available predictors, including the top-performing SignalP. .. _deepsig: https://github.com/BolognaBiocomp/deepsig ]]></help> <expand macro="citation"></expand> </tool>