Mercurial > repos > iuc > filter_tabular

comparison filter_tabular.xml @ 13:4d5aae46f850 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
author iuc
date Thu, 19 Aug 2021 19:39:58 +0000
parents 6544e4b87a4f
children
comparison
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12:37cde8134c6a 13:4d5aae46f850
1 <tool id="filter_tabular" name="Filter Tabular" version="3.1.2"> 1 <tool id="filter_tabular" name="Filter Tabular" version="3.3.0">
2 <description></description> 2 <description></description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 python '$__tool_directory__/filter_tabular.py' 9 python '$__tool_directory__/filter_tabular.py'
10 -i '$input' 10 -i '$input'
11 $comment_char
11 -j '$filter_json' 12 -j '$filter_json'
12 -o '$output' 13 -o '$output'
13 ]]></command> 14 ]]></command>
14 <configfiles> 15 <configfiles>
15 <configfile name="filter_json"> 16 <configfile name="filter_json">
16 #import json 17 #import json
18 #set $dataset_name = $input.element_identifier
17 @LINEFILTERS@ 19 @LINEFILTERS@
18 #if $input_filters: 20 #if $input_filters:
19 #echo $json.dumps($input_filters) 21 #echo $json.dumps($input_filters)
20 #end if 22 #end if
21 </configfile> 23 </configfile>
22 </configfiles> 24 </configfiles>
23 <inputs> 25 <inputs>
24 <param name="input" type="data" format="tabular" label="Tabular Dataset to filter"/> 26 <param name="input" type="data" format="tabular" label="Tabular Dataset to filter"/>
27 <param name="comment_char" type="boolean" truevalue="--comment_char '#'" falsevalue="" checked="true" label="exclude lines starting with #"/>
25 <expand macro="macro_line_filters" /> 28 <expand macro="macro_line_filters" />
26 </inputs> 29 </inputs>
27 <outputs> 30 <outputs>
28 <data format="tabular" name="output" /> 31 <data format="tabular" name="output" />
29 </outputs> 32 </outputs>
137 <param name="add" value="prepend"/> 140 <param name="add" value="prepend"/>
138 </conditional> 141 </conditional>
139 </repeat> 142 </repeat>
140 <output name="output" file="filtered_customers_results.tsv"/> 143 <output name="output" file="filtered_customers_results.tsv"/>
141 </test> 144 </test>
145 <test>
146 <param name="input" ftype="tabular" value="IEDB.tsv"/>
147 <param name="comment_char" value="False"/>
148 <repeat name="linefilters">
149 <conditional name="filter">
150 <param name="filter_type" value="replace"/>
151 <param name="column" value="c1"/>
152 <param name="regex_pattern" value="#ID"/>
153 <param name="regex_replace" value="ID"/>
154 </conditional>
155 </repeat>
156 <repeat name="linefilters">
157 <conditional name="filter">
158 <param name="filter_type" value="select_column_slices"/>
159 <param name="columns" value="6,0:6,8,-3"/>
160 </conditional>
161 </repeat>
162 <repeat name="linefilters">
163 <conditional name="filter">
164 <param name="filter_type" value="append_dataset_name"/>
165 </conditional>
166 </repeat>
167 <output name="output" file="filtered_IEDB.tsv"/>
168 </test>
142 </tests> 169 </tests>
143 <help><![CDATA[ 170 <help><![CDATA[
144 ============== 171 ==============
145 Filter Tabular 172 Filter Tabular
146 ============== 173 ==============