comparison PDAUG_AA_Property_Based_Peptide_Descriptor/PDAUG_AA_Property_Based_Peptide_Descriptor.xml @ 0:fbd01647d7e6 draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 02:15:42 +0000
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children ce7100c6884f
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-1:000000000000 0:fbd01647d7e6
1 <tool id="pdaug_aa_property_based_peptide_descriptor" name="PDAUG AA Property Based Peptide Descriptor" version="0.1.0">
2 <description>Calculates amino acid property based peptide descriptors</description>
3
4 <requirements>
5 <requirement type="package" version="0.24.2">pandas</requirement>
6 <requirement type="package" version="4.2.1">modlamp</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1" level="fatal" />
10 </stdio>
11 <command detect_errors="exit_code"><![CDATA[
12
13
14 python '$__tool_directory__/PDAUG_AA_Property_Based_Peptide_Descriptor.py' '$SelDescriptor.Descriptor'
15
16 --InFile '$InFile'
17
18 #if $SelDescriptor.Descriptor == 'AutoCorrCal'
19 --WindowSize $SelDescriptor.WindowSize
20 --ScaleName $SelDescriptor.ScaleName
21 #end if
22
23 #if $SelDescriptor.Descriptor == 'CrossCorrCal'
24 --WindowSize $SelDescriptor.WindowSize
25 --ScaleName $SelDescriptor.ScaleName
26 #end if
27
28 #if $SelDescriptor.Descriptor == 'CalculateMovement'
29 --WindowSize $SelDescriptor.WindowSize
30 --Angle $SelDescriptor.Angle
31 --Modality $SelDescriptor.Modality
32 --ScaleName $SelDescriptor.ScaleName
33 #end if
34
35 #if $SelDescriptor.Descriptor == 'GlobalCal'
36 --WindowSize $SelDescriptor.WindowSize
37 --Modality $SelDescriptor.Modality
38 --ScaleName $SelDescriptor.ScaleName
39 #end if
40
41 #if $SelDescriptor.Descriptor == 'ProfileCal'
42 --ProfType $SelDescriptor.ProfType
43 --WindowSize $SelDescriptor.WindowSize
44 --ScaleName $SelDescriptor.ScaleName
45 #end if
46
47 #if $SelDescriptor.Descriptor == 'ArcCal'
48 --Modality $SelDescriptor.Modality
49 #end if
50
51 --OutFile $output1
52
53 ]]></command>
54
55
56 <inputs>
57
58
59 <param name="InFile" type="data" label="Input fasta file" format="fasta" argument= "--InFile" help="Input fasta file with peptide sequence"/>
60
61 <conditional name='SelDescriptor' >
62
63 <param name="Descriptor" type="select" label="Descriptor type" argument="">
64 <option value="AutoCorrCal">AutoCorrCal</option>
65 <option value="CrossCorrCal">CrossCorCal</option>
66 <option value="CalculateMovement">CalculateMovement</option>
67 <option value="GlobalCal">GlobalCal</option>
68 <option value="ProfileCal">ProfileCal</option>
69 <option value="ArcCal">ArcCal</option>
70 </param>
71
72 <when value="AutoCorrCal">
73 <param name="WindowSize" type="integer" label="Correlation window" value="7" argument="--WindowSize" help="Correlation window for descriptor calculation in a sliding window approach" />
74 <param name="ScaleName" type="text" label="AA Scale Name" value="Eisenberg" argument="--ScaleName" help="Name of the amino acid scale to be loaded."/>
75 </when>
76
77 <when value="CrossCorrCal">
78 <param name="WindowSize" type="integer" label="Correlation window" value="7" argument="--WindowSize" help="correlation window for descriptor calculation in a sliding window approach" />
79 <param name="ScaleName" type="text" value="Eisenberg" label="AA Scale Name" argument="--ScaleName" help="Name of the amino acid scale to be loaded."/>
80 </when>
81
82 <when value="CalculateMovement">
83 <param name="WindowSize" type="integer" label="AA window" value="1000" argument="--WindowSize" help="Amino acid (AA) window in which to calculate the moment."/>
84 <param name="Angle" type="integer" label="Angle" value="100" argument="--Angle" help=" Angle in which to calculate the moment. 100 for alpha helices, 180 for beta sheets."/>
85 <param name="Modality" type="select" argument="--Modality" label="Modality" help="Calculate respectively maximum or mean hydrophobic moment. If all, moments for all windows are returned.">
86 <option value="all"> All</option>
87 <option value="max" selected="true">Max</option>
88 <option value="mean">Mean</option>
89 </param>
90 <param name="ScaleName" type="text" value="Eisenberg" label = "AA scale name" argument="--ScaleName" help="Name of the amino acid scale to be loaded."/>
91 </when>
92
93 <when value="GlobalCal">
94 <param name="WindowSize" type="integer" value="1000" argument="--lenmin_s" label="AA window " help="Amino acid(AA) window in which to calculate the moment. If the sequence is shorter than the window, the length of the sequence is taken"/>
95 <param name="Modality" type="select" argument="--Modality" label="Modality" help="Calculate respectively maximum or mean hydrophobic moment.">
96 <option value="max" selected="true">Max</option>
97 <option value="mean">Mean</option>
98 </param>
99 <param name="ScaleName" type="text" value="Eisenberg" label = "AA scale name" argument="--ScaleName" help="Name of the amino acid scale to be loaded."/>
100
101 </when>
102
103 <when value="ProfileCal">
104 <param name="ProfType" type="select" argument="--ProfType" label="Profile type" help="Profile type of profile, available: ‘H’ for hydrophobicity or ‘uH’ for hydrophobic moment" >
105 <option value="H" selected="true">H</option>
106 <option value="uH">uH</option>
107 </param>
108
109 <param name="WindowSize" type="integer" value="7" argument="--lenmin_s" label="Window Size" help="Size of sliding window used"/>
110 <param name="ScaleName" value="Eisenberg" type="text" label = "AA scale name" argument="--ScaleName" help="Name of the amino acid scale to be loaded."/>
111 </when>
112
113 <when value="ArcCal">
114 <param name="Modality" type="select" argument="--Modality" label="Modality" help="modality of the arc to calculate, to choose between max and mean.">
115 <option value="max" selected="true">Max</option>
116 <option value="mean">Mean</option>
117 </param>
118 </when>
119 </conditional>
120 </inputs>
121
122
123 <outputs>
124 <data name='output1' format='tabular' label="${tool.name} on $on_string - ${SelDescriptor.Descriptor} (tabular)" />
125 </outputs>
126 <tests>
127 <test>
128 <param name="InFile" value="test.fasta"/>
129 <param name="Descriptor" value="AutoCorrCal"/>
130 <param name="WindowSize" value="7"/>
131 <param name="ScaleName" value="Eisenberg"/>
132 <output name="output1" file="out1.tsv"/>
133 </test>
134 <test>
135 <param name="InFile" value="test.fasta"/>
136 <param name="Descriptor" value="CrossCorrCal"/>
137 <param name="WindowSize" value="7"/>
138 <param name="ScaleName" value="Eisenberg"/>
139 <output name="output1" file="out2.tsv"/>
140 </test>
141 <test>
142 <param name="InFile" value="test.fasta"/>
143 <param name="Descriptor" value="CalculateMovement"/>
144 <param name="WindowSize" value="1000"/>
145 <param name="ScaleName" value="Eisenberg"/>
146 <param name="Angle" value="100"/>
147 <param name="Modality" value="max"/>
148 <output name="output1" file="out3.tsv"/>
149 </test>
150 <test>
151 <param name="InFile" value="test.fasta"/>
152 <param name="Descriptor" value="GlobalCal"/>
153 <param name="WindowSize" value="1000"/>
154 <param name="ScaleName" value="Eisenberg"/>
155 <param name="Modality" value="max"/>
156 <output name="output1" file="out4.tsv"/>
157 </test>
158
159 <test>
160 <param name="InFile" value="test.fasta"/>
161 <param name="Descriptor" value="ProfileCal"/>
162 <param name="WindowSize" value="7"/>
163 <param name="ScaleName" value="Eisenberg"/>
164 <param name="ProfType" value="H"/>
165 <output name="output1" file="out5.tsv"/>
166 </test>
167
168 <test>
169 <param name="InFile" value="test.fasta"/>
170 <param name="Descriptor" value="ArcCal"/>
171 <param name="Modality" value="max"/>
172 <output name="output1" file="out6.tsv"/>
173 </test>
174 </tests>
175 <help><![CDATA[
176 .. class:: infomark
177
178 **What it does**
179
180 This tool calculates 6 different types of peptide descriptors.
181
182 * **AutoCorCal** This option calculates descriptor via auto-correlating the amino acid values for a given descriptor scale.
183 * **CrosCorCal** This option calculates descriptor via cross-correlating the amino acid values for a given descriptor scale.
184 * **CalculateMovement** This option calculates descriptor based on the maximum or mean movement of the amino acid values for a given descriptor scale and window.
185 * **GlobalCal** This option calculates descriptors via calculating a global / window averaging descriptor value of a given AA scale.
186 * **ProfileCal** This tool calculates description via calculating hydrophobicity or hydrophobic moment profiles for given sequences and fitting for slope and intercept.
187 * **ArcCal** This option calculates descriptors via calculating property arcs as seen in the helical wheel plot. This method work for binary amino acid scales only.
188
189 -----
190
191 **Inputs**
192 **1** AutoCorrCal
193 * **--Infile** Input fasta file with peptides.
194 * **--WindowSize** Correlation window for descriptor calculation in a sliding window approach.
195 * **--ScaleName** Method to load amino acid values from a given scale.
196
197 **2** CrossCorrCal
198 * **--Infile** Input fasta file with peptides.
199 * **--WindowSize** Correlation window for descriptor calculation in a sliding window approach
200 * **--ScaleName** Method to load amino acid values from a given scale.
201
202 **3** CalculateMovement
203 * **--Infile** Input fasta file with peptides.
204 * **--WindowSize** Amino acid window in which to calculate the moment. If the sequence is shorter than the window, the length of the sequence is taken. So if the default window of 1000 is chosen, for all sequences shorter than 1000, the global hydrophobic moment will be calculated. Otherwise, the maximal hydrophiobic moment for the chosen window size found in the sequence will be returned.
205 * **--ScaleName** Method to load amino acid values from a given scale.
206 * **--Angle** Angle in which to calculate the moment. 100 for alpha-helices, 180 for beta sheets.
207 * **--Modality** Calculate respectively maximum or mean hydrophobic moment. If all, moments for all windows are returned.
208
209 **4** GlobalCal
210 * **--Infile** Input fasta file with peptides.
211 * **--Modality** Calculate respectively maximum or mean hydrophobic moment.
212 * **--WindowSize** amino acid window in which to calculate the moment. If the sequence is shorter than the window, the length of the sequence is taken.
213 * **--ScaleName** Method to load amino acid values from a given scale.
214
215 **5** ProfileCal
216 * **--Infile** Input fasta file with peptides.
217 * **--Infile** Input fasta file with peptides.
218 * **--ProfType** prof_type of the profile, available: ‘H’ for hydrophobicity or ‘uH’ for a hydrophobic moment
219 * **--WindowSize** {int} size of sliding window used (odd-numbered).
220
221 **6** ArcCal
222 * **--Modality** Modality of the arc to calculate, to choose between “max” and “mean”.
223
224 -----
225
226 **Outputs**
227 * Return tabular file with the descriptors.]]></help>
228
229
230 <citations>
231 <citation type="bibtex">
232 @misc{PDAUGGITHUB,
233 author = {Joshi, Jayadev and Blankenberg, Daniel},
234 year = {2020},
235 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
236 publisher = {GitHub},
237 journal = {GitHub repository},
238 url =
239 {https://github.com/jaidevjoshi83/pdaug.git},
240 }
241 </citation>
242
243 <citation type="bibtex">
244 @article{müller_gabernet_hiss_schneider_2017,
245 title={modlAMP: Python for antimicrobial peptides},
246 volume={33},
247 DOI={10.1093/bioinformatics/btx285},
248 number={17},
249 journal={Bioinformatics},
250 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert},
251 year={2017},
252 pages={2753–2755}
253 }
254 </citation>
255
256 </citations>
257
258 </tool>
259
260
261