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comparison filter_spades_repeats.xml @ 0:ddd1e15df88c draft

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author aaronpetkau
date Sat, 04 Jul 2015 09:45:30 -0400
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1 <tool id="filter_spades_repeat" name="Filter SPAdes repeats" version="1.0.0">
2 <description>Remove short and repeat contigs/scaffolds</description>
3 <requirements>
4 <requirement type="package" version="5.18.1">perl</requirement>
5 </requirements>
6 <command interpreter="perl">nml_filter_spades_repeats.pl -i $fasta_input -t $tab_input -c $cov_cutoff -r $rep_cutoff -l $len_cutoff -o $output_with_repeats -u $output_without_repeats -n $repeat_sequences_only -e $cov_len_cutoff -f $discarded_sequences -s $summary
7 </command>
8
9 <inputs>
10 <param name="fasta_input" type="data" format="fasta" label="Contigs or scaffolds file" help="Contigs/Scaffolds output file from Spades" />
11 <param name="tab_input" type="data" format="tabular" label="Stats file" help="Enter the corresponding stats file of the fasta file input above" />
12 <param name="cov_cutoff" type="float" value="0.33" min="0" label="Coverage cut-off ratio" help="This is the average coverage ratio cutoff. For example: if the average coverage is 100 and a coverage cut-off ratio of 0.5 is used, then any contigs with coverage lower than 50 will be eliminated." />
13 <param name="rep_cutoff" type="float" value="1.75" min="0" label="Repeat cut-off ratio" help="This is the coverage ratio cutoff to determine repeats in contigs. For exmaple: if the average coverage is 100 and a repeat cut-off ratio of 1.75 is used, then any contigs with coverage more than or equal to 175 will be marked as repeats." />
14 <param name="len_cutoff" type="integer" value="1000" min="0" label="Length cut-off" help="Contigs with length under the chosen cut-off will be eliminated." />
15 <param name="cov_len_cutoff" type="integer" value="5000" min="0" label="Length for average coverage calculation" help="Only contigs above this length will be used to calculate the average coverage." />
16 <param name="keep_leftover" type="select" label="Print out a fasta file containing the discarded sequences?">
17 <option value="yes">Yes</option>
18 <option value="no">No</option>
19 </param>
20 <param name="print_summary" type="select" label="Print out a summary of all the results?">
21 <option value="yes">Yes</option>
22 <option value="no">No</option>
23 </param>
24 </inputs>
25 <outputs>
26 <data format="fasta" name="output_with_repeats" label="Filtered sequences (with repeats)" />
27 <data format="fasta" name="output_without_repeats" label="Filtered sequences (no repeats)" />
28 <data format="fasta" name="repeat_sequences_only" label="Repeat sequences" />
29 <data format="fasta" name="discarded_sequences" label="Discarded sequences">
30 <filter>keep_leftover == "yes"</filter>
31 </data>
32 <data format="txt" name="summary" label="Results summary">
33 <filter>print_summary == "yes"</filter>
34 </data>
35 </outputs>
36
37
38
39
40 <help>
41 ================
42 **What it does**
43 ================
44
45 Using the output of SPAdes (a fasta and a stats file, either from contigs or scaffolds), it filters the fasta files, discarding all sequences that are under a given length or under a calculated coverage. Repeated contigs are detected based on coverage.
46
47 --------------------------------------
48
49 ==========
50 **Output**
51 ==========
52
53 - **Filtered sequences (with repeats)**
54 - Will contain the filtered contigs/scaffolds including the repeats. These are the sequences that passed the length and minumum coverage cutoffs.
55 - For workflows, this output is named **output_with_repeats**
56 - **Filtered sequences (no repeats)**
57 - Will contain the filtered contigs/scaffolds excluding the repeats. These are the sequences that passed the length, minimum coverage and repeat cutoffs.
58 - For workflows, this output is named **output_without_repeats**
59 - **Repeat sequences**
60 - Will contain the repeated contigs/scaffolds only. These are the sequences that were exluded for having high coverage (determined by the repeat cutoff).
61 - For workflows, this output is named **repeat_sequences_only**
62 - **Discarded sequences**
63 - If selected, will contain the discarded sequences. These are the sequences that fell below the length and minumum coverage cutoffs, and got discarded.
64 - For workflows, this output is named **discarded_sequences**
65 - **Results summary** : If selected, will contain a summary of all the results.
66
67 ------------------------------------------
68
69 ============
70 **Example**
71 ============
72
73 Stats file input:
74 ------------------
75
76 +------------+------------+------------+
77 |#name |length |coverage |
78 +============+============+============+
79 |NODE_1 |2500 |15.5 |
80 +------------+------------+------------+
81 |NODE_2 |102 |3.0 |
82 +------------+------------+------------+
83 |NODE_3 |1300 |50.0 |
84 +------------+------------+------------+
85 |NODE_4 |1000 |2.3 |
86 +------------+------------+------------+
87 |NODE_5 |5000 |14.3 |
88 +------------+------------+------------+
89 |NODE_6 |450 |25.2 |
90 +------------+------------+------------+
91
92 User Inputs:
93 ------------
94
95 - Coverage cut-off ratio = 0.33
96 - Repeat cut-off ratio = 1.75
97 - Length cut-off = 500
98 - Length for average coverage calculation = 1000
99
100 Calculations:
101 -------------
102
103 **Average coverage will be calculatd based on contigs with length >= 1000bp**
104
105
106 - Average coverage = 15.5 + 50.0 + 2.3 + 14.3 / 4 = 20.5
107
108 **Contigs that have coverage in the lower 1/3 of the average coverage will be eliminated.**
109
110 - Coverage cut-off = 20.5 * 0.33 = 6.8
111
112 **Contigs with high coverage (larger than 1.75 times the average coverage) are considered to be repeated contigs.**
113
114 - Repeat cut-off = 20.5 * 1.75 = 35.9
115
116 **Number of copies are calculated by dividing the sequence coverage by the average coverage.**
117
118 - Number of repeats for NODE_3 = 50 / 20.5 = 2 copies
119
120
121 Output (in fasta format):
122 --------------------------
123
124 **Filtered sequences (with repeats)**
125
126 ::
127
128 >NODE_1
129 >NODE_3 (2 copies)
130 >NODE_5
131
132 **Filtered sequences (no repeats)**
133
134 ::
135
136 >NODE_1
137 >NODE_5
138
139 **Repeat sequences**
140
141 ::
142
143 >NODE_3 (2 copies)
144
145 **Discarded sequences**
146
147 ::
148
149 >NODE_2
150 >NODE_4
151 >NODE_6
152
153 ---------------------------------------
154
155
156
157
158 </help>
159
160 </tool>