Mercurial > repos > jay > pdaug_peptide_core_functions

comparison PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml @ 0:e743e76b8991 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author jay
date Wed, 28 Oct 2020 02:07:30 +0000
parents
children 562dc0806625
comparison
equal deleted inserted replaced
-1:000000000000 0:e743e76b8991
1 <tool id="pdaug_peptide_core_functions" name="PDAUG Peptide Core Functions" version="0.1.0">
2 <description> Peptide sequence related core functions </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 </requirements>
8 <stdio>
9 <exit_code range="1" level="fatal" />
10 </stdio>
11 <command detect_errors="exit_code"><![CDATA[
12
13
14 python '$__tool_directory__/PDAUG_Peptide_Core_Functions.py' '$SelCoreFunction.CoreFunction'
15
16 --InFile '$InFile'
17
18 #if $SelCoreFunction.CoreFunction == 'mutateAA'
19 --nr $SelCoreFunction.nr
20 --Prob $SelCoreFunction.prob
21 #end if
22
23 #if $SelCoreFunction.CoreFunction == 'filteraa'
24 --FilterAA $SelCoreFunction.FilterAA
25 #end if
26
27 --FastOut '$output1'
28
29 ]]></command>
30
31 <inputs>
32
33 <param name="InFile" type="data" format="fasta" label="Input file" argument= "--InFile" help="Input fasta file with peptides"/>
34
35 <conditional name='SelCoreFunction' >
36
37 <param name="CoreFunction" type="select" label="Analysis options" argument="">
38 <option value="mutateAA">Mutate Amino Acid</option>
39 <option value="filterduplicates">Filter Duplicates</option>
40 <option value="keepnaturalaa">Keep Naturalaa</option>
41 <option value="filteraa">Filter Amino Acid</option>
42 </param>
43
44 <when value="mutateAA">
45 <param name="nr" type="integer" label="Number of mutations" value="3" argument="--nr" help="Number of mutations"/>
46 <param name="prob" type="float" label="Probability" value="1.0" argument="--Prob" help="Probability of mutating a sequence" />
47 </when>
48
49 <when value="filterduplicates">
50 </when>
51
52 <when value="keepnaturalaa">
53 </when>
54
55 <when value="filteraa">
56 <param name="FilterAA" type="text" value="eisenberg" label="Filter AA" argument="--FilterAA" help="Amino acids to be filtered" />
57 </when>
58
59 </conditional>
60 </inputs>
61
62 <outputs>
63 <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelCoreFunction.CoreFunction} (fasta)" />
64 </outputs>
65 <tests>
66 <test>
67 <param name="InFile" value="test1.fasta"/>
68 <param name="CoreFunction" value="mutateAA" />
69 <param name="nr" value="3"/>
70 <param name="prob" value="1.0"/>
71 <output name="output1" file="out1.fasta" lines_diff="2"/>
72 </test>
73 <test>
74 <param name="InFile" value="test2.fasta"/>
75 <param name="CoreFunction" value="filterduplicates" />
76 <output name="output1" file="out2.fasta" />
77 </test>
78 <test>
79 <param name="InFile" value="test3.fasta"/>
80 <param name="CoreFunction" value="keepnaturalaa" />
81 <output name="output1" file="out3.fasta" />
82 </test>
83 <test>
84 <param name="InFile" value="test4.fasta"/>
85 <param name="CoreFunction" value="filteraa" />
86 <param name="FilterAA" value="eisenberg" />
87 <output name="output1" file="out4.fasta" />
88 </test>
89 </tests>
90 <help><![CDATA[
91 .. class:: infomark
92
93 **What it does**
94
95 This tool performs some core functions on the peptide sequences and equipped with various options
96
97 * **Mutated Amino Acid** Method to mutate with prob probability an nr of positions per sequence randomly.
98 * **Filter Duplicates** Method to filter duplicates in the sequences from the class attribute sequences.
99 * **Keep Naturalaa** Method to filter out sequences that do not contain natural amino acids. If the sequence contains a character.
100 * **Filter Amino Acid** Method to filter out corresponding names and descriptor values of sequences with given amino acids in the argument list aminoacids.
101
102 -----
103
104 **Inputs**
105
106 1 **Mutate Amino Acid**
107 * **--InFile** takes Fasta file with peptide sequences.
108 * **--nr** Number of mutations.
109 * **--probability** Probability of mutating a sequence.
110
111 2 **Filter Duplicates***
112 * **--InFile** takes Fasta file with peptide sequences.
113
114 3 **Keep Naturalaa**
115 * **--InFile** takes Fasta file with peptide sequences.
116
117 4 **Filter Amino Acid**
118 * **--InFile** takes Fasta file with peptide sequences.
119
120 -----
121
122 **Outputs**
123 * Returns a fasta file.]]></help>
124
125 <citations>
126 <citation type="bibtex">
127 @misc{PDAUGGITHUB,
128 author = {Joshi, Jayadev and Blankenberg, Daniel},
129 year = {2020},
130 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
131 publisher = {GitHub},
132 journal = {GitHub repository},
133 url =
134 {https://github.com/jaidevjoshi83/pdaug.git},
135 }
136 </citation>
137
138 <citation type="bibtex">
139 @article{müller_gabernet_hiss_schneider_2017,
140 title={modlAMP: Python for antimicrobial peptides},
141 volume={33},
142 DOI={10.1093/bioinformatics/btx285},
143 number={17},
144 journal={Bioinformatics},
145 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert},
146 year={2017},
147 pages={2753–2755}
148 }
149 </citation>
150 </citations>
151 </tool>
152
153
154