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comparison obiclean.xml @ 6:fea356c8cd06 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools commit b017355279c18334e66ea8c0c0d7727fbd2876f7
author iuc
date Thu, 13 Nov 2025 10:22:44 +0000
parents c78f86dd30c1
children
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5:c78f86dd30c1 6:fea356c8cd06
58 58
59 .. class:: infomark 59 .. class:: infomark
60 60
61 **What it does** 61 **What it does**
62 62
63 obijoinpairedend aims at joining the two reads of a paired-end library. 63 obiclean is a command that classifies sequence records either as head, internal or singleton.
64 64
65 For this purpose, it concatenates sequence merging the forward read and the reversed-complemented reverse read. 65 For that purpose, two pieces of information are used:
66 66
67 The program uses as input one or two sequences reads files. 67 - sequence record counts
68 - sequence similarities
68 69
69 If two files are used one of them must be specified using the -r option. Sequence records corresponding to the same read pair must be in the same order in the two files. 70 S1 a sequence record is considered as a variant of S2 another sequence record if and only if:
70 If just one file is provided, sequence records are supposed to be all of the same length. The first half of the sequence is used as forward read, the second half is used as the reverse read. 71
72 - count of S1 divided by count of S2 is lesser than the ratio R. R default value is set to 1, and can be adjusted between 0 and 1 with the -r option.
73 - both sequences are related to one another (they can align with some differences, the maximum number of differences can be specified by the -d option).
74
75 Considering S a sequence record, the following properties hold for S tagged as:
76
77 **head:**
78 - there exists at least one sequence record in the dataset that is a variant of S
79 - there exists no sequence record in the dataset such that S is a variant of this sequence record
80
81 **internal:**
82 - there exists at least one sequence record in the dataset such that S is a variant of this sequence record
83
84 **singleton:**
85 - there exists no sequence record in the dataset that is a variant of S
86 - there exists no sequence record in the dataset such that S is a variant of this sequence record
87
88 By default, tagging is done once for the whole dataset, but it can also be done sample by sample by specifying the -s option. In such a case, the counts are extracted from the sample information.
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90 Finally, each sequence record is annotated with three new attributes head, internal and singleton. The attribute values are the numbers of samples in which the sequence record has been classified in this manner.
71 91
72 @OBITOOLS_LINK@ 92 @OBITOOLS_LINK@
73 93
74 ]]> 94 ]]>
75 </help> 95 </help>