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filter_tabular.xml
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filter_tabular.xml
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<tool id="filter_tabular" name="Filter Tabular" version="3.3.0">
<description></description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/filter_tabular.py'
-i '$input'
$comment_char
-j '$filter_json'
-o '$output'
]]></command>
<configfiles>
<configfile name="filter_json">
#import json
#set $dataset_name = $input.element_identifier
@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"/>
<param name="comment_char" type="boolean" truevalue="--comment_char '#'" falsevalue="" checked="true" label="exclude lines starting with #"/>
<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>
<test>
<param name="input" ftype="tabular" value="customers.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="replace"/>
<param name="column" value="c4"/>
<param name="regex_pattern" value=".*@(.*)"/>
<param name="regex_replace" value="\1"/>
<param name="add" value="after"/>
</conditional>
</repeat>
<repeat name="linefilters">
<conditional name="filter">
<param name="filter_type" value="replace"/>
<param name="column" value="c4"/>
<param name="regex_pattern" value=".*(com|org|net)$"/>
<param name="regex_replace" value="\1"/>
<param name="add" value="append"/>
</conditional>
</repeat>
<repeat name="linefilters">
<conditional name="filter">
<param name="filter_type" value="replace"/>
<param name="column" value="c6"/>
<param name="regex_pattern" value="^(\d+)-(\d+)-(\d+)$"/>
<param name="regex_replace" value="\1"/>
<param name="add" value="prepend"/>
</conditional>
</repeat>
<output name="output" file="filtered_customers_results.tsv"/>
</test>
<test>
<param name="input" ftype="tabular" value="IEDB.tsv"/>
<param name="comment_char" value="False"/>
<repeat name="linefilters">
<conditional name="filter">
<param name="filter_type" value="replace"/>
<param name="column" value="c1"/>
<param name="regex_pattern" value="#ID"/>
<param name="regex_replace" value="ID"/>
</conditional>
</repeat>
<repeat name="linefilters">
<conditional name="filter">
<param name="filter_type" value="select_column_slices"/>
<param name="columns" value="6,0:6,8,-3"/>
</conditional>
</repeat>
<repeat name="linefilters">
<conditional name="filter">
<param name="filter_type" value="append_dataset_name"/>
</conditional>
</repeat>
<output name="output" file="filtered_IEDB.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>
<expand macro="citations" />
</tool>