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1 <tool id="subtract_query1" name="Subtract Whole Dataset">
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2 <description>from another dataset</description>
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3 <command interpreter="python">subtract_query.py $input1 $input2 $begin_col $end_col $output</command>
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4 <inputs>
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5 <param format="txt" name="input2" type="data" label="Subtract" help="Second dataset" />
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6 <param format="txt" name="input1" type="data" label="from" help="First dataset" />
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7 <param name="begin_col" type="data_column" data_ref="input1" force_select="False" label="Restrict subtraction between 'begin column'" />
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8 <param name="end_col" type="data_column" data_ref="input1" force_select="False" label="and 'end column'" help="Specifying columns for restricting subtraction is available only for tabular formatted datasets" />
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9 </inputs>
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10 <outputs>
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11 <data format="input" name="output" metadata_source="input1" />
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12 </outputs>
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13 <tests>
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14 <!-- Subtract 2 non-tabular files with no column restrictions. -->
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15 <!-- Cannot figure out why this test won't pass, it works in real time...
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16 <test>
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17 <param name="input1" value="1.txt" />
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18 <param name="input2" value="2.txt" />
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19 <param name="begin_col" value="None" />
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20 <param name="end_col" value="None" />
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21 <output name="output" file="subtract-query-1.dat" />
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22 </test>
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23 -->
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24 <!-- Subtract 2 tabular files with no column restrictions. -->
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25 <test>
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26 <param name="input1" value="eq-showbeginning.dat" />
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27 <param name="input2" value="eq-showtail.dat" />
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28 <param name="begin_col" value="None" />
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29 <param name="end_col" value="None" />
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30 <output name="output" file="subtract-query-2.dat" />
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31 </test>
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32 <!-- Subtract 2 tabular files with column restrictions. -->
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33 <test>
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34 <param name="input1" value="eq-showbeginning.dat" />
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35 <param name="input2" value="eq-removebeginning.dat" />
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36 <param name="begin_col" value="c1" />
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37 <param name="end_col" value="c3" />
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38 <output name="output" file="subtract-query-3.dat" />
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39 </test>
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40 <!-- Subtract a non-tabular file from a tabular file with no column restrictions. -->
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41 <test>
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42 <param name="input1" value="eq-showbeginning.dat" />
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43 <param name="input2" value="2.txt" />
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44 <param name="begin_col" value="None" />
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45 <param name="end_col" value="None" />
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46 <output name="output" file="subtract-query-4.dat" />
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47 </test>
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48 </tests>
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49 <help>
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50
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51 .. class:: infomark
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52
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53 **TIP:** This tool complements the tool in the **Operate on Genomic Intervals** tool set which subtracts the intervals of two datasets.
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54
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55
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56 -----
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57
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58 **Syntax**
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59
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60 This tool subtracts an entire dataset from another dataset.
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61
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62 - Any text format is valid.
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63 - If both dataset formats are tabular, you may restrict the subtraction to specific columns **contained in both datasets** and the resulting dataset will include only the columns specified.
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64 - The begin column must be less than or equal to the end column. If it is not, begin column is switched with end column.
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65 - If begin column is specified but end column is not, end column will default to begin_column (and vice versa).
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66 - All blank and comment lines are skipped and not included in the resulting dataset (comment lines are lines beginning with a # character).
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67 - Duplicate lines are eliminated from both dataset prior to subtraction. If any duplicate lines were eliminated from the first dataset, the number is displayed in the resulting history item.
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68
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69 -----
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70
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71 **Example**
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72
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73 If this is the **First dataset**::
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74
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75 chr1 4225 19670
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76 chr10 6 8
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77 chr1 24417 24420
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78 chr6_hla_hap2 0 150
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79 chr2 1 5
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80 chr10 2 10
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81 chr1 30 55
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82 chrY 1 20
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83 chr1 1225979 42287290
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84 chr10 7 8
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85
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86 and this is the **Second dataset**::
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87
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88 chr1 4225 19670
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89 chr10 6 8
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90 chr1 24417 24420
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91 chr6_hla_hap2 0 150
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92 chr2 1 5
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93 chr1 30 55
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94 chrY 1 20
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95 chr1 1225979 42287290
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96
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97 Subtracting the **Second dataset** from the **First dataset** (including all columns) will yield::
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98
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99 chr10 7 8
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100 chr10 2 10
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101
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102 Conversely, subtracting the **First dataset** from the **Second dataset** (including all columns) will result in an empty dataset.
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103
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104 Subtracting the **Second dataset** from the **First dataset** (restricting to columns c1 and c2) will yield::
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105
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106 chr10 7
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107 chr10 2
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108
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109 </help>
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110 </tool> |
