Mercurial > repos > jay > pdaug_peptide_data_access
comparison PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml @ 0:6c12ca9f5d88 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 01:59:25 +0000 |
parents | |
children | f85327600c11 |
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1 <tool id="pdaug_peptide_data_access" name="PDAUG Peptide Data Access" version="0.1.0"> | |
2 <description>Fetch peptide data from inbuild datasets and public databases</description> | |
3 | |
4 <requirements> | |
5 <requirement type="package" version="0.24.2">pandas</requirement> | |
6 <requirement type="package" version="4.1.2">modlamp</requirement> | |
7 <requirement type="package" version="8.0.21">mysql-connector-python</requirement> | |
8 </requirements> | |
9 <stdio> | |
10 <exit_code range="1" level="fatal" /> | |
11 </stdio> | |
12 <command detect_errors="exit_code"><![CDATA[ | |
13 | |
14 python '$__tool_directory__/PDAUG_Peptide_Data_Access.py' -d '$SelectDatasets.DataBaseType' -o '$output1' | |
15 | |
16 #if $SelectDatasets.DataBaseType == "query_apd" | |
17 -L $SelectDatasets.list1 | |
18 #end if | |
19 | |
20 #if $SelectDatasets.DataBaseType == "query_camp" | |
21 -L $SelectDatasets.list2 | |
22 #end if | |
23 | |
24 ]]></command> | |
25 | |
26 | |
27 <inputs> | |
28 | |
29 <conditional name="SelectDatasets"> | |
30 | |
31 <param name="DataBaseType" type="select" label="Datasets" argument="--DataBaseType" help="Name of the data set."> | |
32 <option value="AMPvsTM" selected="true" > AMPvsTM </option> | |
33 <option value="AMPvsUniProt" > AMPvsUniProt </option> | |
34 <option value="ACPvsTM"> ACPvsTM </option> | |
35 <option value="ACPvsRandom"> ACPvsRandom </option> | |
36 <option value="query_apd"> Query APD Database</option> | |
37 <option value="query_camp" > Query CAMP Database </option> | |
38 </param> | |
39 | |
40 | |
41 | |
42 <when value="query_apd"> | |
43 <param name="list1" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" /> | |
44 </when> | |
45 | |
46 <when value="query_camp"> | |
47 <param name="list2" type='text' argument="-List" label="List of integers as IDs" help="List of integers as IDs" /> | |
48 </when> | |
49 | |
50 </conditional> | |
51 | |
52 | |
53 </inputs> | |
54 | |
55 <outputs> | |
56 <data name='output1' format='tabular' label="${tool.name} $on_string - ${SelectDatasets.DataBaseType} (tabular)" /> | |
57 </outputs> | |
58 | |
59 <tests> | |
60 <test> | |
61 <param name="DataBaseType" value="AMPvsTM"/> | |
62 <output name="output1" file="out.tsv"/> | |
63 </test> | |
64 | |
65 <test> | |
66 <param name="DataBaseType" value="query_apd"/> | |
67 <param name="list1" value="4,5,6" /> | |
68 <output name="output1" file="apd.tsv" lines_diff="8"/> | |
69 </test> | |
70 | |
71 <test> | |
72 <param name="DataBaseType" value="query_camp"/> | |
73 <param name="list2" value="3,4,5,9" /> | |
74 <output name="output1" file="camp.tsv" lines_diff="10"/> | |
75 </test> | |
76 | |
77 | |
78 </tests> | |
79 | |
80 <help><![CDATA[ | |
81 .. class:: infomark | |
82 | |
83 **What it does** | |
84 | |
85 This tool returns inbuild peptide data sets. | |
86 | |
87 * **AMPvsTM** This option returns Antimicrobial peptides and transmembrane sequences. | |
88 * **AMPvsUniProt** This option returns AMPs from the APD3 and other peptides from the UniProt database. | |
89 * **ACPvsTM** This option returns anticancer peptides (CancerPPD) and helical transmembrane sequences. | |
90 * **ACPvsRandom** This option returns anticancer peptides (CancerPPD) and random scrambled AMP sequences. | |
91 | |
92 ----- | |
93 | |
94 **Inputs** | |
95 * **--DataBaseType** Takes dataset name as input. | |
96 | |
97 ----- | |
98 | |
99 **Outputs** | |
100 * Returns a tabular file with peptide sequences and class labels.]]></help> | |
101 | |
102 | |
103 <citations> | |
104 <citation type="bibtex"> | |
105 @misc{PDAUGGITHUB, | |
106 author = {Joshi, Jayadev and Blankenberg, Daniel}, | |
107 year = {2020}, | |
108 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, | |
109 publisher = {GitHub}, | |
110 journal = {GitHub repository}, | |
111 url = | |
112 {https://github.com/jaidevjoshi83/pdaug.git}, | |
113 } | |
114 </citation> | |
115 | |
116 <citation type="bibtex"> | |
117 @article{müller_gabernet_hiss_schneider_2017, | |
118 title={modlAMP: Python for antimicrobial peptides}, | |
119 volume={33}, | |
120 DOI={10.1093/bioinformatics/btx285}, | |
121 number={17}, | |
122 journal={Bioinformatics}, | |
123 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, | |
124 year={2017}, | |
125 pages={2753–2755} | |
126 } | |
127 </citation> | |
128 </citations> | |
129 </tool> | |
130 | |
131 | |
132 |