[2] | 1 | <tool id="subtract_query1" name="Subtract Whole Query"> |
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| 2 | <description>from another query</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 query" /> |
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| 6 | <param format="txt" name="input1" type="data" label="from" help="First query" /> |
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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 queries" /> |
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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 queries. |
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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 query from another query. |
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| 61 | |
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| 62 | - Any text format is valid. |
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| 63 | - If both query formats are tabular, you may restrict the subtraction to specific columns **contained in both queries** and the resulting query 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 query (comment lines are lines beginning with a # character). |
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| 67 | - Duplicate lines are eliminated from both queries prior to subtraction. If any duplicate lines were eliminated from the first query, 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 query**:: |
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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 query**:: |
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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 query** from the **First query** (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 query** from the **Second query** (including all columns) will result in an empty dataset. |
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| 103 | |
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| 104 | Subtracting the **Second query** from the **First query** (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> |
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