Mercurial > repos > devteam > subtract_query
diff subtract_query.xml @ 0:8a3448727cec draft
Imported from capsule None
author | devteam |
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date | Tue, 01 Apr 2014 09:12:49 -0400 |
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children | f58ba0382c26 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/subtract_query.xml Tue Apr 01 09:12:49 2014 -0400 @@ -0,0 +1,131 @@ +<tool id="subtract_query1" name="Subtract Whole Dataset" version="0.1"> + <description>from another dataset</description> + <requirements> + <requirement type="package" version="0.7.1">bx-python</requirement> + <requirement type="package" version="1.0.0">galaxy-ops</requirement> + </requirements> + <command interpreter="python"> + subtract_query.py $input1 $input2 $begin_col $end_col $output + #if str($ignore_empty_end_cols) == 'true': + --ignore-empty-end-cols + #end if + + </command> + <inputs> + <param format="txt" name="input2" type="data" label="Subtract" help="Second dataset" /> + <param format="txt" name="input1" type="data" label="from" help="First dataset" /> + <param name="begin_col" type="data_column" data_ref="input1" force_select="False" label="Restrict subtraction between 'begin column'" /> + <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" /> + <param name="ignore_empty_end_cols" type="boolean" label="Ignore empty columns and whitespace at end of line when subtracting"/> + </inputs> + <outputs> + <data format="input" name="output" metadata_source="input1" /> + </outputs> + <tests> + <!-- Subtract 2 non-tabular files with no column restrictions. --> + <!-- Cannot figure out why this test won't pass, it works in real time... --> + <!-- + <test> + <param name="input1" value="1.txt" /> + <param name="input2" value="2.txt" /> + <param name="begin_col" value="None" /> + <param name="end_col" value="None" /> + <output name="output" file="subtract-query-1.dat" /> + </test> + --> + <!-- Subtract 2 tabular files with no column restrictions. --> + <test> + <param name="input1" value="eq-showbeginning.dat" /> + <param name="input2" value="eq-showtail.dat" /> + <param name="begin_col" value="None" /> + <param name="end_col" value="None" /> + <output name="output" file="subtract-query-2.dat" /> + </test> + <!-- Subtract 2 tabular files with column restrictions. --> + <test> + <param name="input1" value="eq-showbeginning.dat" /> + <param name="input2" value="eq-removebeginning.dat" /> + <param name="begin_col" value="c1" /> + <param name="end_col" value="c3" /> + <output name="output" file="subtract-query-3.dat" /> + </test> + <!-- Subtract a non-tabular file from a tabular file with no column restrictions. --> + <test> + <param name="input1" value="eq-showbeginning.dat" /> + <param name="input2" value="2.txt" /> + <param name="begin_col" value="None" /> + <param name="end_col" value="None" /> + <output name="output" file="subtract-query-4.dat" /> + </test> + <!-- Subtract 2 tabular files with no column restrictions, ignoring empty end columns. --> + <test> + <param name="input1" value="eq-showbeginning_e.dat" /> + <param name="input2" value="eq-showtail.dat" /> + <param name="begin_col" value="None" /> + <param name="end_col" value="None" /> + <param name="ignore_empty_end_cols" value="true" /> + <output name="output" file="subtract-query-2.dat" /> + </test> + </tests> + <help> + +.. class:: infomark + +**TIP:** This tool complements the tool in the **Operate on Genomic Intervals** tool set which subtracts the intervals of two datasets. + + +----- + +**Syntax** + +This tool subtracts an entire dataset from another dataset. + +- Any text format is valid. +- 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. +- The begin column must be less than or equal to the end column. If it is not, begin column is switched with end column. +- If begin column is specified but end column is not, end column will default to begin_column (and vice versa). +- All blank and comment lines are skipped and not included in the resulting dataset (comment lines are lines beginning with a # character). +- 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. + +----- + +**Example** + +If this is the **First dataset**:: + + chr1 4225 19670 + chr10 6 8 + chr1 24417 24420 + chr6_hla_hap2 0 150 + chr2 1 5 + chr10 2 10 + chr1 30 55 + chrY 1 20 + chr1 1225979 42287290 + chr10 7 8 + +and this is the **Second dataset**:: + + chr1 4225 19670 + chr10 6 8 + chr1 24417 24420 + chr6_hla_hap2 0 150 + chr2 1 5 + chr1 30 55 + chrY 1 20 + chr1 1225979 42287290 + +Subtracting the **Second dataset** from the **First dataset** (including all columns) will yield:: + + chr10 7 8 + chr10 2 10 + +Conversely, subtracting the **First dataset** from the **Second dataset** (including all columns) will result in an empty dataset. + +Subtracting the **Second dataset** from the **First dataset** (restricting to columns c1 and c2) will yield:: + + chr10 7 + chr10 2 + + </help> +</tool> \ No newline at end of file