Mercurial > repos > jay > pdaug_peptide_core_functions

comparison PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml @ 6:6822d43a5f84 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 e8c8198105af7eab636fb2405e5ff335539ca14b"
author jay
date Sun, 31 Jan 2021 02:17:01 +0000
parents 562dc0806625
children 851602577d38
comparison
equal deleted inserted replaced
5:48eedcb9bfa7 6:6822d43a5f84
34 34
35 <conditional name='SelCoreFunction' > 35 <conditional name='SelCoreFunction' >
36 36
37 <param name="CoreFunction" type="select" label="Analysis options" argument=""> 37 <param name="CoreFunction" type="select" label="Analysis options" argument="">
38 <option value="mutateAA">Mutate Amino Acid</option> 38 <option value="mutateAA">Mutate Amino Acid</option>
39 <option value="filterduplicates">Filter Duplicates</option> 39 <option value="filterduplicates">Filter Duplicates Peptides</option>
40 <option value="keepnaturalaa">Keep Naturalaa</option> 40 <option value="keepnaturalaa">Remove Peptides With Unatural Amino Acids</option>
41 <option value="filteraa">Filter Amino Acid</option> 41 <option value="filteraa">Filter Peptides With Specific Amino Acid</option>
42 </param> 42 </param>
43 43
44 <when value="mutateAA"> 44 <when value="mutateAA">
45 <param name="nr" type="integer" label="Number of mutations" value="3" argument="--nr" help="Number of mutations"/> 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" /> 46 <param name="prob" type="float" label="Probability" value="1.0" argument="--Prob" help="Probability of mutating a sequence" />
92 92
93 **What it does** 93 **What it does**
94 94
95 This tool performs some core functions on the peptide sequences and equipped with various options 95 This tool performs some core functions on the peptide sequences and equipped with various options
96 96
97 * **Mutated Amino Acid** Method to mutate with prob probability an nr of positions per sequence randomly. 97 * **Mutate 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. 98 * **Filter Duplicates Peptides** 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. 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. 100 * **Filter Amino Acid** Method to filter out corresponding names and descriptor values of sequences with given amino acids in the argument list aminoacids.
101 101
102 ----- 102 -----
103 103
106 1 **Mutate Amino Acid** 106 1 **Mutate Amino Acid**
107 * **--InFile** takes Fasta file with peptide sequences. 107 * **--InFile** takes Fasta file with peptide sequences.
108 * **--nr** Number of mutations. 108 * **--nr** Number of mutations.
109 * **--probability** Probability of mutating a sequence. 109 * **--probability** Probability of mutating a sequence.
110 110
111 2 **Filter Duplicates*** 111 2 **Filter Duplicates Peptides***
112 * **--InFile** takes Fasta file with peptide sequences. 112 * **--InFile** takes Fasta file with peptide sequences.
113 113
114 3 **Keep Naturalaa** 114 3 **Remove Peptides With Unatural Amino Acids**
115 * **--InFile** takes Fasta file with peptide sequences. 115 * **--InFile** takes Fasta file with peptide sequences.
116 116
117 4 **Filter Amino Acid** 117 4 **Filter Peptides With Specific Amino Acid**
118 * **--InFile** takes Fasta file with peptide sequences. 118 * **--InFile** takes Fasta file with peptide sequences.
119 119
120 ----- 120 -----
121 121
122 **Outputs** 122 **Outputs**