Mercurial > repos > jay > pdaug_peptide_core_functions
annotate PDAUG_Peptide_Core_Functions/PDAUG_Peptide_Core_Functions.xml @ 7:851602577d38 draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
author | jay |
---|---|
date | Sun, 09 Jan 2022 04:32:43 +0000 |
parents | 6822d43a5f84 |
children |
rev | line source |
---|---|
0
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
1 <tool id="pdaug_peptide_core_functions" name="PDAUG Peptide Core Functions" version="0.1.0"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
2 <description> Peptide sequence related core functions </description> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
3 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
4 <requirements> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
5 <requirement type="package" version="0.24.2">pandas</requirement> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
6 <requirement type="package" version="4.1.2">modlamp</requirement> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
7 </requirements> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
8 <stdio> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
9 <exit_code range="1" level="fatal" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
10 </stdio> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
11 <command detect_errors="exit_code"><![CDATA[ |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
12 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
13 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
14 python '$__tool_directory__/PDAUG_Peptide_Core_Functions.py' '$SelCoreFunction.CoreFunction' |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
15 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
16 --InFile '$InFile' |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
17 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
18 #if $SelCoreFunction.CoreFunction == 'mutateAA' |
1
562dc0806625
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
jay
parents:
0
diff
changeset
|
19 --nr '$SelCoreFunction.nr' |
562dc0806625
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
jay
parents:
0
diff
changeset
|
20 --Prob '$SelCoreFunction.prob' |
0
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
21 #end if |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
22 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
23 #if $SelCoreFunction.CoreFunction == 'filteraa' |
7
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
24 --FilterAA 'filterAA' |
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
25 #end if |
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
26 |
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
27 #if $SelCoreFunction.CoreFunction == 'filterduplicates' |
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
28 --FilterAA 'filterduplicates' |
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
29 #end if |
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
30 |
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
31 #if $SelCoreFunction.CoreFunction == 'keepnaturalaa' |
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
32 --FilterAA 'keepnaturalaa' |
0
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
33 #end if |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
34 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
35 --FastOut '$output1' |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
36 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
37 ]]></command> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
38 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
39 <inputs> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
40 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
41 <param name="InFile" type="data" format="fasta" label="Input file" argument= "--InFile" help="Input fasta file with peptides"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
42 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
43 <conditional name='SelCoreFunction' > |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
44 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
45 <param name="CoreFunction" type="select" label="Analysis options" argument=""> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
46 <option value="mutateAA">Mutate Amino Acid</option> |
6
6822d43a5f84
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
1
diff
changeset
|
47 <option value="filterduplicates">Filter Duplicates Peptides</option> |
6822d43a5f84
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
1
diff
changeset
|
48 <option value="keepnaturalaa">Remove Peptides With Unatural Amino Acids</option> |
6822d43a5f84
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
1
diff
changeset
|
49 <option value="filteraa">Filter Peptides With Specific Amino Acid</option> |
0
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
50 </param> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
51 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
52 <when value="mutateAA"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
53 <param name="nr" type="integer" label="Number of mutations" value="3" argument="--nr" help="Number of mutations"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
54 <param name="prob" type="float" label="Probability" value="1.0" argument="--Prob" help="Probability of mutating a sequence" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
55 </when> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
56 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
57 <when value="filterduplicates"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
58 </when> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
59 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
60 <when value="keepnaturalaa"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
61 </when> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
62 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
63 <when value="filteraa"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
64 <param name="FilterAA" type="text" value="eisenberg" label="Filter AA" argument="--FilterAA" help="Amino acids to be filtered" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
65 </when> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
66 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
67 </conditional> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
68 </inputs> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
69 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
70 <outputs> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
71 <data name='output1' format='fasta' label="${tool.name} on $on_string - ${SelCoreFunction.CoreFunction} (fasta)" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
72 </outputs> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
73 <tests> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
74 <test> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
75 <param name="InFile" value="test1.fasta"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
76 <param name="CoreFunction" value="mutateAA" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
77 <param name="nr" value="3"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
78 <param name="prob" value="1.0"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
79 <output name="output1" file="out1.fasta" lines_diff="2"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
80 </test> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
81 <test> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
82 <param name="InFile" value="test2.fasta"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
83 <param name="CoreFunction" value="filterduplicates" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
84 <output name="output1" file="out2.fasta" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
85 </test> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
86 <test> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
87 <param name="InFile" value="test3.fasta"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
88 <param name="CoreFunction" value="keepnaturalaa" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
89 <output name="output1" file="out3.fasta" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
90 </test> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
91 <test> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
92 <param name="InFile" value="test4.fasta"/> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
93 <param name="CoreFunction" value="filteraa" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
94 <param name="FilterAA" value="eisenberg" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
95 <output name="output1" file="out4.fasta" /> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
96 </test> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
97 </tests> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
98 <help><![CDATA[ |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
99 .. class:: infomark |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
100 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
101 **What it does** |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
102 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
103 This tool performs some core functions on the peptide sequences and equipped with various options |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
104 |
6
6822d43a5f84
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
1
diff
changeset
|
105 * **Mutate Amino Acid** Method to mutate with prob probability an nr of positions per sequence randomly. |
6822d43a5f84
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
1
diff
changeset
|
106 * **Filter Duplicates Peptides** Method to filter duplicates in the sequences from the class attribute sequences. |
0
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
107 * **Keep Naturalaa** Method to filter out sequences that do not contain natural amino acids. If the sequence contains a character. |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
108 * **Filter Amino Acid** Method to filter out corresponding names and descriptor values of sequences with given amino acids in the argument list aminoacids. |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
109 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
110 ----- |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
111 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
112 **Inputs** |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
113 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
114 1 **Mutate Amino Acid** |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
115 * **--InFile** takes Fasta file with peptide sequences. |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
116 * **--nr** Number of mutations. |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
117 * **--probability** Probability of mutating a sequence. |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
118 |
6
6822d43a5f84
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
1
diff
changeset
|
119 2 **Filter Duplicates Peptides*** |
0
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
120 * **--InFile** takes Fasta file with peptide sequences. |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
121 |
6
6822d43a5f84
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
1
diff
changeset
|
122 3 **Remove Peptides With Unatural Amino Acids** |
0
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
123 * **--InFile** takes Fasta file with peptide sequences. |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
124 |
6
6822d43a5f84
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
jay
parents:
1
diff
changeset
|
125 4 **Filter Peptides With Specific Amino Acid** |
0
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
126 * **--InFile** takes Fasta file with peptide sequences. |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
127 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
128 ----- |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
129 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
130 **Outputs** |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
131 * Returns a fasta file.]]></help> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
132 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
133 <citations> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
134 <citation type="bibtex"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
135 @misc{PDAUGGITHUB, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
136 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
137 year = {2020}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
138 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
139 publisher = {GitHub}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
140 journal = {GitHub repository}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
141 url = |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
142 {https://github.com/jaidevjoshi83/pdaug.git}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
143 } |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
144 </citation> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
145 |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
146 <citation type="bibtex"> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
147 @article{müller_gabernet_hiss_schneider_2017, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
148 title={modlAMP: Python for antimicrobial peptides}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
149 volume={33}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
150 DOI={10.1093/bioinformatics/btx285}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
151 number={17}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
152 journal={Bioinformatics}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
153 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
154 year={2017}, |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
155 pages={2753–2755} |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
156 } |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
157 </citation> |
e743e76b8991
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff
changeset
|
158 </citations> |
7
851602577d38
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 32b9c48c81639a81be24bb3e2f48dc0a81c0deca"
jay
parents:
6
diff
changeset
|
159 </tool> |