Mercurial > repos > devteam > subtract_query
diff subtract_query.xml @ 3:f58ba0382c26 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/subtract_query commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
| author | devteam |
|---|---|
| date | Thu, 22 Jun 2017 18:51:44 -0400 |
| parents | 8a3448727cec |
| children |
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--- a/subtract_query.xml Fri Dec 18 19:39:32 2015 -0500 +++ b/subtract_query.xml Thu Jun 22 18:51:44 2017 -0400 @@ -1,87 +1,89 @@ <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> - + <description>from another dataset</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command><![CDATA[ +python '$__tool_directory__/subtract_query.py' +'$input1' +'$input2' +$begin_col +$end_col +'$output' +#if str($ignore_empty_end_cols) == 'true': + --ignore-empty-end-cols +#end if + ]]></command> + <inputs> + <param name="input2" type="data" format="txt" label="Subtract" help="Second dataset" /> + <param name="input1" type="data" format="txt" 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 name="output" format_source="input1" 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="" /> + <param name="end_col" value="" /> + <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="" /> + <param name="end_col" value="" /> + <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="" /> + <param name="end_col" value="" /> + <param name="ignore_empty_end_cols" value="true" /> + <output name="output" file="subtract-query-2.dat" /> + </test> + </tests> + <help><![CDATA[ .. 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. +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. +- 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). @@ -102,7 +104,7 @@ chr1 30 55 chrY 1 20 chr1 1225979 42287290 - chr10 7 8 + chr10 7 8 and this is the **Second dataset**:: @@ -117,7 +119,7 @@ Subtracting the **Second dataset** from the **First dataset** (including all columns) will yield:: - chr10 7 8 + chr10 7 8 chr10 2 10 Conversely, subtracting the **First dataset** from the **Second dataset** (including all columns) will result in an empty dataset. @@ -126,6 +128,5 @@ chr10 7 chr10 2 - - </help> -</tool> \ No newline at end of file + ]]></help> +</tool>