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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepsig commit 8d5424b11bc4d5a4112b030dc38016e4d8b60e21
author iuc
date Tue, 23 May 2023 17:04:14 +0000
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-1:000000000000 0:8016ec0e41a1
1 <?xml version="1.0"?>
2 <tool id="deepsig" name="DeepSig" version="@TOOL_VERSION@+galaxy0" profile="21.05">
3 <description>signal peptides predictor</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">deepsig</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 deepsig
12 -f '$input_fasta'
13 -o '$output'
14 -k $organism
15 -m $output_format
16 -t \${GALAXY_SLOTS:-1}
17
18 ]]></command>
19
20 <inputs>
21 <param name="input_fasta" argument="-f" type="data" format="fasta" label="Protein sequences"/>
22 <param name="organism" argument="-k" type="select" label="Taxonomic domain">
23 <option value="euk" selected="true">Eukaryotes</option>
24 <option value="gramp">Gram-positive</option>
25 <option value="gramn">Gram-negative</option>
26 </param>
27
28 <param name="output_format" argument="-m" type="select" label="output_format">
29 <option value="gff3" selected="true">GFF3</option>
30 <option value="json">JSON</option>
31 </param>
32 </inputs>
33
34 <outputs>
35 <data name="output" format="gff3" label="DeepSig on ${on_string}">
36 <change_format>
37 <when input="output_format" value="json" format="json"/>
38 </change_format>
39 </data>
40 </outputs>
41
42 <tests>
43 <test expect_num_outputs="1">
44 <param name="input_fasta" value="G5ED35.fasta"/>
45 <param name="organism" value="euk"/>
46 <param name="output_format" value="gff3"/>
47 <output name="output" ftype="gff3">
48 <assert_contents>
49 <has_text text="sp|G5ED35|TTR52_CAEEL"/>
50 <has_text text="evidence=ECO:0000256"/>
51 </assert_contents>
52 </output>
53 </test>
54 <test expect_num_outputs="1">
55 <param name="input_fasta" value="G5ED35.fasta"/>
56 <param name="organism" value="euk"/>
57 <param name="output_format" value="json"/>
58 <output name="output" ftype="json">
59 <assert_contents>
60 <has_text text='"sequence": "MSRFLIYFLPFFIYSGNVLSKTSCLMATGVLKCPTDPEAVKKVHIDLWDEDSLPLESDDLMGRTWSDRNGNFQVTGCASDFGPINTPDPYLYIQHNCPHRDSNATNPIQIDVIPLFLPSIVRLGNVYLDRYLEDY"'/>
61 </assert_contents>
62 </output>
63 </test>
64 </tests>
65
66 <help><![CDATA[
67 deepsig_ Predictor of signal peptides in proteins based on deep learning.
68 DeepSig is a novel approach to predict signal peptides in proteins based on
69 deep learning and sequence labelling methods. The proposed approach was
70 evaluated and compared with other available predictors, including the top-performing SignalP.
71
72 .. _deepsig: https://github.com/BolognaBiocomp/deepsig
73 ]]></help>
74
75 <expand macro="citation"></expand>
76 </tool>