Mercurial > repos > iuc > filter_tabular
diff filter_tabular.xml @ 0:6fbd9d25ceef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 74915fc9cee746bbce1c4b507e13231259de177d
author | iuc |
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date | Tue, 18 Jul 2017 09:06:47 -0400 |
parents | |
children | cd2a99849f8b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_tabular.xml Tue Jul 18 09:06:47 2017 -0400 @@ -0,0 +1,130 @@ +<tool id="filter_tabular" name="Filter Tabular" version="1.0.0"> + <description></description> + + <macros> + <import>macros.xml</import> + </macros> + + <requirements> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python '$__tool_directory__/filter_tabular.py' + -i '$input' + -j '$filter_json' + -o '$output' + ]]></command> + <configfiles> + <configfile name="filter_json"> +#import json +@LINEFILTERS@ +#if $input_filters: +#echo $json.dumps($input_filters) +#end if + </configfile> + </configfiles> + <inputs> + <param name="input" type="data" format="tabular" label="Tabular Dataset to filter"/> + <expand macro="macro_line_filters" /> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <tests> + <test> + <param name="input" ftype="tabular" value="pets.tsv"/> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="regex"/> + <param name="regex_pattern" value="^\d+"/> + <param name="regex_action" value="include_find"/> + </conditional> + </repeat> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="append_line_num"/> + </conditional> + </repeat> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="select_columns"/> + <param name="columns" value="7,2,3,4,1"/> + </conditional> + </repeat> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="replace"/> + <param name="column" value="c4"/> + <param name="regex_pattern" value="(\d+)/(\d+)/(\d+)"/> + <param name="regex_replace" value="19\3-\2-\1"/> + </conditional> + </repeat> + <output name="output" file="filtered_people_results.tsv"/> + </test> + <test> + <param name="input" ftype="tabular" value="pets.tsv"/> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="comment"/> + <param name="comment_char" value="35"/> + </conditional> + </repeat> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="regex"/> + <param name="regex_pattern" value="^\d+"/> + <param name="regex_action" value="include_find"/> + </conditional> + </repeat> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="append_line_num"/> + </conditional> + </repeat> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="select_columns"/> + <param name="columns" value="c7,c5,c6"/> + </conditional> + </repeat> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="normalize"/> + <param name="columns" value="c2,c3"/> + <param name="separator" value=","/> + </conditional> + </repeat> + <repeat name="linefilters"> + <conditional name="filter"> + <param name="filter_type" value="regex"/> + <param name="regex_pattern" value="^\d+\t\t"/> + <param name="regex_action" value="exclude_match"/> + </conditional> + </repeat> + <output name="output" file="filtered_pets_results.tsv"/> + </test> + + </tests> + <help><![CDATA[ +============== +Filter Tabular +============== + + Filter a tabular dataset by applying line filters as it is being read. + Multiple filters may be used with each filter using the result of the previous filter. + +**Inputs** + + A tabular dataset. + + +**Outputs** + + A filtered tabular dataset. + + +@LINEFILTERS_HELP@ + +@LINEFILTERS_HELP_EXAMPLE@ + + ]]></help> +</tool>