annotate deepsig.xml @ 0:8d9746627f77 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig commit 8d5424b11bc4d5a4112b030dc38016e4d8b60e21

<?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>