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comparison mytools/sampline.xml @ 7:f0dc65e7f6c0

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author xuebing
date Fri, 09 Mar 2012 19:59:07 -0500
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6:094f377db4e5 7:f0dc65e7f6c0
1 <tool id="sampline" name="sample">
2 <description>records from a file</description>
3 <command interpreter="python">sampline.py --input=$input --output=$out_file1 --nSample=$nSample --recSize=$recSize --nSkip=$nSkip $replacement</command>
4 <inputs>
5 <param name="input" format="txt" type="data" label="Original file"/>
6 <param name="nSample" size="10" type="integer" value="100" label="Number of records to sample"/>
7 <param name="recSize" size="10" type="integer" value="1" label="Number of lines per record"/>
8 <param name="nSkip" size="10" type="integer" value="0" label="Number of top lines to output directly (without sampling)"/>
9 <param name="replacement" label="Sampling with replacement" type="boolean" truevalue="--replacement" falsevalue="" checked="False"/>
10 </inputs>
11 <outputs>
12 <data format="input" name="out_file1" />
13 </outputs>
14 <tests>
15 <test>
16 <output name="out_file1" file="testmap.sampled"/>
17 <param name="input" value="test.map" ftype="TXT"/>
18 <param name="nSample" value="100"/>
19 <param name="recSize" value="1" />
20 <param name="nSkip" value="0" />
21 <param name="replacement" value=""/>
22 </test>
23 </tests>
24 <help>
25
26 **What it does**
27
28 This tool selects random records from a file. Each record is defined by a fixed number of lines.
29
30 - When doing over-sampling, --replacement option is enforced by default.
31
32 -----
33
34 **Example 1: sampling from a BED file**
35
36 parameters::
37
38 1 line per record, sampling 5 lines, without replacement, output line 1 (track name) directly
39
40 Input::
41
42 track name=test.bed
43 chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 -
44 chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
45 chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 +
46 chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
47 chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 -
48 chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
49 chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
50 chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
51 chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 +
52 chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 -
53
54 Output::
55
56 track name=test.bed
57 chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 -
58 chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 +
59 chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 -
60 chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 +
61 chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 +
62
63 **Example 2: sampling reads from a fastq file**
64
65 parameters::
66
67 4 line per record, sampling 3 records, without replacement
68
69 Input::
70
71 @SRR066787.2496 WICMT-SOLEXA:8:1:28:2047 length=36
72 NNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
73 +SRR066787.2496 WICMT-SOLEXA:8:1:28:2047 length=36
74 !!%!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
75 @SRR066787.2497 WICMT-SOLEXA:8:1:28:463 length=36
76 GTGATTAAGAAGAGACTGGCATCACTAAGGTGACAT
77 +SRR066787.2497 WICMT-SOLEXA:8:1:28:463 length=36
78 @A=BBCBBAA@:@:@@@:,?AB:B?BB=*2:@=?AA
79 @SRR066787.2498 WICMT-SOLEXA:8:1:28:704 length=36
80 GAACCCAATTTTCAAAGAAGTGTGACTGCTTGTTTC
81 +SRR066787.2498 WICMT-SOLEXA:8:1:28:704 length=36
82 =?BAABBACCCCAA9>>A=>A?A;;@A>ABBABBB:
83 @SRR066787.2499 WICMT-SOLEXA:8:1:28:997 length=36
84 CGACTTCAGGCTCTCGCTAGCCTTCGCTTGACTGAC
85 +SRR066787.2499 WICMT-SOLEXA:8:1:28:997 length=36
86 BCCBCCB?A1ACAC>;@CCAAABB?8=BA>@?B?@:
87 @SRR066787.2500 WICMT-SOLEXA:8:1:28:582 length=36
88 TCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTC
89 +SRR066787.2500 WICMT-SOLEXA:8:1:28:582 length=36
90 ?.?.=9C8CCC:BACBCBC?CCC@CBBBCBBACAC8
91
92 Output::
93
94 @SRR066787.2497 WICMT-SOLEXA:8:1:28:463 length=36
95 GTGATTAAGAAGAGACTGGCATCACTAAGGTGACAT
96 +SRR066787.2497 WICMT-SOLEXA:8:1:28:463 length=36
97 @A=BBCBBAA@:@:@@@:,?AB:B?BB=*2:@=?AA
98 @SRR066787.2499 WICMT-SOLEXA:8:1:28:997 length=36
99 CGACTTCAGGCTCTCGCTAGCCTTCGCTTGACTGAC
100 +SRR066787.2499 WICMT-SOLEXA:8:1:28:997 length=36
101 BCCBCCB?A1ACAC>;@CCAAABB?8=BA>@?B?@:
102 @SRR066787.2500 WICMT-SOLEXA:8:1:28:582 length=36
103 TCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTC
104 +SRR066787.2500 WICMT-SOLEXA:8:1:28:582 length=36
105 ?.?.=9C8CCC:BACBCBC?CCC@CBBBCBBACAC8
106
107 </help>
108 </tool>