Mercurial > repos > iuc > deepsig
comparison deepsig.xml @ 0:8d9746627f77 draft default tip
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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-1:000000000000 | 0:8d9746627f77 |
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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> |