Mercurial > repos > jay > pdaug_peptide_core_functions
comparison PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml @ 6:6822d43a5f84 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author | jay |
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date | Sun, 31 Jan 2021 02:17:01 +0000 |
parents | 562dc0806625 |
children | 851602577d38 |
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5:48eedcb9bfa7 | 6:6822d43a5f84 |
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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** |