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