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1 <tool id="trimmer" name="Trim" version="0.0.1">
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2 <description>leading or trailing characters</description>
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3 <command interpreter="python">
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4 trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1
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5 </command>
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6 <inputs>
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7 <param format="tabular,txt" name="input1" type="data" label="this dataset"/>
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8 <param name="col" type="integer" value="0" label="Trim this column only" help="0 = process entire line" />
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9 <param name="start" type="integer" size="10" value="1" label="Trim from the beginning to this position" help="1 = do not trim the beginning"/>
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10 <param name="end" type="integer" size="10" value="0" label="Remove everything from this position to the end" help="0 = do not trim the end"/>
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11 <param name="fastq" type="select" label="Is input dataset in fastq format?" help="If set to YES, the tool will not trim evenly numbered lines (0, 2, 4, etc...)">
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12 <option selected="true" value="">No</option>
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13 <option value="-q">Yes</option>
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14 </param>
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15 <param name="ignore" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not trimmed">
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16 <option value="62">></option>
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17 <option value="64">@</option>
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18 <option value="43">+</option>
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19 <option value="60"><</option>
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20 <option value="42">*</option>
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21 <option value="45">-</option>
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22 <option value="61">=</option>
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23 <option value="124">|</option>
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24 <option value="63">?</option>
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25 <option value="36">$</option>
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26 <option value="46">.</option>
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27 <option value="58">:</option>
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28 <option value="38">&</option>
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29 <option value="37">%</option>
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30 <option value="94">^</option>
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31 <option value="35">#</option>
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32 </param>
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33 </inputs>
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34 <outputs>
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35 <data name="out_file1" format="input" metadata_source="input1"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input1" value="trimmer_tab_delimited.dat"/>
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40 <param name="col" value="0"/>
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41 <param name="start" value="1"/>
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42 <param name="end" value="13"/>
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43 <param name="ignore" value="62"/>
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44 <param name="fastq" value="No"/>
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45 <output name="out_file1" file="trimmer_a_f_c0_s1_e13_i62.dat"/>
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46 </test>
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47 <test>
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48 <param name="input1" value="trimmer_tab_delimited.dat"/>
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49 <param name="col" value="2"/>
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50 <param name="start" value="1"/>
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51 <param name="end" value="2"/>
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52 <param name="ignore" value="62"/>
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53 <param name="fastq" value="No"/>
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54 <output name="out_file1" file="trimmer_a_f_c2_s1_e2_i62.dat"/>
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55 </test>
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56
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57 </tests>
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58
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59 <help>
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60
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61
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62 **What it does**
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63
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64 Trims specified number of characters from a dataset or its field (if dataset is tab-delimited).
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65
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66 -----
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67
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68 **Example 1**
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69
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70 Trimming this dataset::
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71
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72 1234567890
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73 abcdefghijk
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74
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75 by setting **Trim from the beginning to this position** to *2* and **Remove everything from this position to the end** to *6* will produce::
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76
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77 23456
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78 bcdef
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79
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80 -----
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81
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82 **Example 2**
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83
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84 Trimming column 2 of this dataset::
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85
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86 abcde 12345 fghij 67890
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87 fghij 67890 abcde 12345
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88
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89 by setting **Trim content of this column only** to *2*, **Trim from the beginning to this position** to *2*, and **Remove everything from this position to the end** to *4* will produce::
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90
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91 abcde 234 fghij 67890
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92 fghij 789 abcde 12345
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93
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94 -----
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95
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96 **Trimming FASTQ datasets**
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97
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98 This tool can be used to trim sequences and quality strings in fastq datasets. This is done by selected *Yes* from the **Is input dataset in fastq format?** dropdown. If set to *Yes*, the tool will skip all even numbered lines (see warning below). For example, trimming last 5 bases of this dataset::
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99
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100 @081017-and-081020:1:1:1715:1759
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101 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC
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102 +
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103 II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B
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104
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105 cab done by setting **Remove everything from this position to the end** to 31::
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106
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107 @081017-and-081020:1:1:1715:1759
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108 GGACTCAGATAGTAATCCACGCTCCTTTAAA
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109 +
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110 II#IIIIIII$5+.(9IIIIIII$%*$G$A3
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111
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112 **Note** that headers are skipped.
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113
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114 .. class:: warningmark
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115
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116 **WARNING:** This tool will only work on properly formatted fastq datasets where (1) each read and quality string occupy one line and (2) '@' (read header) and "+" (quality header) lines are evenly numbered like in the above example.
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117
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118
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119 </help>
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120 </tool>
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