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1 <tool id="subtract_query1" name="Subtract Whole Dataset" version="0.1">
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2 <description>from another dataset</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
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6 </requirements>
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7 <command interpreter="python">
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8 subtract_query.py $input1 $input2 $begin_col $end_col $output
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9 #if str($ignore_empty_end_cols) == 'true':
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10 --ignore-empty-end-cols
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11 #end if
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12
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13 </command>
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14 <inputs>
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15 <param format="txt" name="input2" type="data" label="Subtract" help="Second dataset" />
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16 <param format="txt" name="input1" type="data" label="from" help="First dataset" />
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17 <param name="begin_col" type="data_column" data_ref="input1" force_select="False" label="Restrict subtraction between 'begin column'" />
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18 <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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19 <param name="ignore_empty_end_cols" type="boolean" label="Ignore empty columns and whitespace at end of line when subtracting"/>
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20 </inputs>
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21 <outputs>
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22 <data format="input" name="output" metadata_source="input1" />
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23 </outputs>
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24 <tests>
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25 <!-- Subtract 2 non-tabular files with no column restrictions. -->
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26 <!-- Cannot figure out why this test won't pass, it works in real time... -->
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27 <!--
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28 <test>
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29 <param name="input1" value="1.txt" />
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30 <param name="input2" value="2.txt" />
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31 <param name="begin_col" value="None" />
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32 <param name="end_col" value="None" />
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33 <output name="output" file="subtract-query-1.dat" />
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34 </test>
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35 -->
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36 <!-- Subtract 2 tabular files with no column restrictions. -->
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37 <test>
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38 <param name="input1" value="eq-showbeginning.dat" />
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39 <param name="input2" value="eq-showtail.dat" />
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40 <param name="begin_col" value="None" />
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41 <param name="end_col" value="None" />
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42 <output name="output" file="subtract-query-2.dat" />
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43 </test>
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44 <!-- Subtract 2 tabular files with column restrictions. -->
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45 <test>
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46 <param name="input1" value="eq-showbeginning.dat" />
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47 <param name="input2" value="eq-removebeginning.dat" />
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48 <param name="begin_col" value="c1" />
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49 <param name="end_col" value="c3" />
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50 <output name="output" file="subtract-query-3.dat" />
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51 </test>
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52 <!-- Subtract a non-tabular file from a tabular file with no column restrictions. -->
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53 <test>
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54 <param name="input1" value="eq-showbeginning.dat" />
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55 <param name="input2" value="2.txt" />
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56 <param name="begin_col" value="None" />
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57 <param name="end_col" value="None" />
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58 <output name="output" file="subtract-query-4.dat" />
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59 </test>
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60 <!-- Subtract 2 tabular files with no column restrictions, ignoring empty end columns. -->
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61 <test>
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62 <param name="input1" value="eq-showbeginning_e.dat" />
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63 <param name="input2" value="eq-showtail.dat" />
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64 <param name="begin_col" value="None" />
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65 <param name="end_col" value="None" />
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66 <param name="ignore_empty_end_cols" value="true" />
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67 <output name="output" file="subtract-query-2.dat" />
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68 </test>
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69 </tests>
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70 <help>
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71
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72 .. class:: infomark
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73
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74 **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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75
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76
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77 -----
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78
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79 **Syntax**
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80
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81 This tool subtracts an entire dataset from another dataset.
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82
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83 - Any text format is valid.
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84 - 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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85 - 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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86 - If begin column is specified but end column is not, end column will default to begin_column (and vice versa).
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87 - 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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88 - 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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89
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90 -----
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91
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92 **Example**
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93
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94 If this is the **First dataset**::
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95
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96 chr1 4225 19670
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97 chr10 6 8
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98 chr1 24417 24420
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99 chr6_hla_hap2 0 150
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100 chr2 1 5
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101 chr10 2 10
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102 chr1 30 55
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103 chrY 1 20
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104 chr1 1225979 42287290
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105 chr10 7 8
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106
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107 and this is the **Second dataset**::
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108
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109 chr1 4225 19670
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110 chr10 6 8
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111 chr1 24417 24420
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112 chr6_hla_hap2 0 150
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113 chr2 1 5
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114 chr1 30 55
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115 chrY 1 20
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116 chr1 1225979 42287290
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117
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118 Subtracting the **Second dataset** from the **First dataset** (including all columns) will yield::
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119
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120 chr10 7 8
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121 chr10 2 10
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122
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123 Conversely, subtracting the **First dataset** from the **Second dataset** (including all columns) will result in an empty dataset.
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124
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125 Subtracting the **Second dataset** from the **First dataset** (restricting to columns c1 and c2) will yield::
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126
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127 chr10 7
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128 chr10 2
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129
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130 </help>
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131 </tool> |
