Mercurial > repos > jay > pdaug_sequence_property_based_descriptors
comparison PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.xml @ 0:6b6aec52638d draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:23:51 +0000 |
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children | 7dc979925e31 |
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1 <tool id="pdaug_sequence_property_based_descriptors" name="PDAUG Sequence Property Based Descriptors" version="0.1.0"> | |
2 <description>Calculates sequence based descriptors of the peptide sequences</description> | |
3 | |
4 <requirements> | |
5 <requirement type="package" version="2.7.18">python</requirement> | |
6 <requirement type="package" version="0.24.2">pandas</requirement> | |
7 <requirement type="package" version="1.0">pydpi</requirement> | |
8 </requirements> | |
9 <stdio> | |
10 <exit_code range="1" level="fatal" /> | |
11 </stdio> | |
12 <command detect_errors="exit_code"><![CDATA[ | |
13 | |
14 python '$__tool_directory__/PDAUG_Sequence_Property_Based_Descriptors.py' --InFile '$input1' | |
15 | |
16 --DesType '$SelectDiscriptor.DesType' | |
17 | |
18 #if '$SelectDiscriptor.DesType' == 'PAAC' | |
19 --Lamda '$SelectDiscriptor.Lamda' | |
20 --Weight '$SelectDiscriptor.Weight' | |
21 #end if | |
22 | |
23 #if $SelectDiscriptor.DesType == 'APAAC' | |
24 --Lamda '$SelectDiscriptor.Lamda' | |
25 --Weight '$SelectDiscriptor.Weight' | |
26 #end if | |
27 | |
28 #if $SelectDiscriptor.DesType == 'All' | |
29 --Lamda '$SelectDiscriptor.Lamda' | |
30 --Weight '$SelectDiscriptor.Weight' | |
31 #end if | |
32 | |
33 | |
34 -O '$output1' | |
35 | |
36 ]]></command> | |
37 | |
38 <inputs> | |
39 | |
40 <param name="input1" type="data" format="fasta" label="Input fasta file" help="Input fasta file with peptides"/> | |
41 | |
42 <conditional name="SelectDiscriptor"> | |
43 | |
44 <param name="DesType" type="select" label="Descriptor Type" argument=""> | |
45 <option value="PAAC">PAAC</option> | |
46 <option value="APAAC">APAAC</option> | |
47 <option value="CTD" selected="true">CTD</option> | |
48 <option value="DPComp">DPComp</option> | |
49 <option value="GearyAuto">GearyAuto</option> | |
50 <option value="MoranAuto">MoranAuto</option> | |
51 <option value="MoreauBrotoAuto">MoreauBrotoAuto</option> | |
52 <option value="QSO">QSO</option> | |
53 <option value="SOCN">SOCN</option> | |
54 <option value="TPComp">TPComp</option> | |
55 <option value="BinaryDescriptor">Binary Descriptor</option> | |
56 <option value="All">All</option> | |
57 </param> | |
58 | |
59 <when value="PAAC" > | |
60 <param name="Lamda" type="integer" label="Lamda" value="50" argument="--Lamda" help="Lamda"/> | |
61 <param name="Weight" type="float" label="Weight" value="0.5" argument="--Weight" help="Weight"/> | |
62 </when> | |
63 | |
64 <when value="APAAC" > | |
65 <param name="Lamda" type="integer" value="50" argument="--Lamda" help="Lamda"/> | |
66 <param name="Weight" type="float" value="0.5" argument="--Weight" help="Weight"/> | |
67 </when> | |
68 | |
69 <when value="All" > | |
70 <param name="Lamda" type="integer" value="50" label="Lamda" argument="--Lamda" help="Lamda"/> | |
71 <param name="Weight" type="float" value="0.5" argument="--Weight" help="Weight"/> | |
72 </when> | |
73 | |
74 <when value="DPComp" > | |
75 </when> | |
76 | |
77 <when value="GearyAuto" > | |
78 </when> | |
79 | |
80 <when value="MoranAuto" > | |
81 </when> | |
82 | |
83 <when value="MoreauBrotoAuto" > | |
84 </when> | |
85 | |
86 <when value="QSO" > | |
87 </when> | |
88 | |
89 <when value="SOCN" > | |
90 </when> | |
91 | |
92 <when value="CTD" > | |
93 </when> | |
94 | |
95 <when value="TPComp" > | |
96 </when> | |
97 | |
98 <when value="BinaryDescriptor" > | |
99 </when> | |
100 | |
101 | |
102 </conditional> | |
103 | |
104 </inputs> | |
105 | |
106 <outputs> | |
107 <data name='output1' format='tabular' label="${tool.name} on $on_string - ${SelectDiscriptor.DesType} (tabular)" /> | |
108 </outputs> | |
109 | |
110 <tests> | |
111 <test> | |
112 <param name="input1" value="positive.fasta"/> | |
113 <param name="DesType" value="All"/> | |
114 <param name="Lamda" value="5"/> | |
115 <param name="Weight" value="0.5"/> | |
116 <output name="output1" value="Out.tsv"/> | |
117 </test> | |
118 | |
119 | |
120 <test> | |
121 <param name="input1" value="positive.fasta"/> | |
122 <param name="DesType" value="BinaryDescriptor"/> | |
123 <output name="output1" value="Out1.tsv"/> | |
124 </test> | |
125 | |
126 </tests> | |
127 <help><![CDATA[ | |
128 .. class:: infomark | |
129 | |
130 **What it does** | |
131 | |
132 This tool calculates sequence property based descriptor for a peptide descriptor. | |
133 | |
134 * **AAC** This option calculates amino acid composition descriptors (20). | |
135 * **DPComp** This option calculates dipeptide composition descriptors (400). | |
136 * **TPComp** This option calculates tri-peptide composition descriptors (8000). | |
137 * **MoreauBrotoAuto** This option calculates Normalized Moreau-Broto autocorrelation descriptors (depend on the given properties, the default is 240). | |
138 * **MoranAuto** This option calculates Moran autocorrelation descriptors (depend on the given properties, the default is 240). | |
139 * **GearyAuto** This option calculates Geary autocorrelation descriptors (depend on the given properties, the default is 240). | |
140 * **CTD** This option calculates Composition, Transition, Distribution descriptors(200). | |
141 * **SOCN** This option calculates sequence order coupling numbers (depend on the choice of maxlag, the default is 60). | |
142 * **QSO** This option calculates quasi-sequence order descriptors (depend on the choice of maxlag, the default is 100). | |
143 * **PAAC** This option calculates pseudo amino acid composition descriptors (depend on the choice of lamda, the default is 50). | |
144 * **APAAC** This option calculates amphiphilic pseudo amino acid composition descriptors, (depend on the choice of lamda, the default is 50). | |
145 * **BinaryDescriptor** This option calculates the binary descriptor of peptide sequences (All the peptides should be the same length). | |
146 * **All** This option calculates all the descriptors except the binary descriptor. | |
147 | |
148 ----- | |
149 | |
150 **Inputs** | |
151 * **--InFile** A fasta file with peptide sequences. | |
152 * **--Lamda** PAAC & APAAC descriptors (depend on the choice of lamda, the default is 50). | |
153 * **--Weight** PAAC & APAAC descriptors (depend on the choice of lamda, the default is 0.5). | |
154 * **--DesType** Select the descriptor type. | |
155 | |
156 | |
157 ----- | |
158 | |
159 **Outputs** | |
160 * Returns tabular file with descriptors. | |
161 | |
162 ]]></help> | |
163 | |
164 <citations> | |
165 <citation type="bibtex"> | |
166 @misc{PDAUGGITHUB, | |
167 author = {Joshi, Jayadev and Blankenberg, Daniel}, | |
168 year = {2020}, | |
169 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, | |
170 publisher = {GitHub}, | |
171 journal = {GitHub repository}, | |
172 url = | |
173 {https://github.com/jaidevjoshi83/pdaug.git}, | |
174 } | |
175 </citation> | |
176 <citation type="bibtex"> | |
177 @article{cao_liang_yan_tan_xu_liu_2013, | |
178 title={PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies}, | |
179 volume={53}, DOI={10.1021/ci400127q}, | |
180 number={11}, | |
181 journal={Journal of Chemical Information and Modeling}, | |
182 author={Cao, Dong-Sheng and Liang, Yi-Zeng and Yan, Jun and Tan, Gui-Shan and Xu, Qing-Song and Liu, Shao}, | |
183 year={2013}, | |
184 pages={3086–3096}} | |
185 </citation> | |
186 </citations> | |
187 </tool> | |
188 | |
189 | |
190 |