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comparison PDAUG_Peptide_Data_Access/PDAUG_Peptide_Data_Access.xml @ 0:6c12ca9f5d88 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 01:59:25 +0000
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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
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132