Mercurial > repos > iuc > filter_tabular
comparison filter_tabular.xml @ 13:4d5aae46f850 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular commit 35576d64a12fa664d72559172c5960c09da2b632"
author | iuc |
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date | Thu, 19 Aug 2021 19:39:58 +0000 |
parents | 6544e4b87a4f |
children | 90f657745fea |
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12:37cde8134c6a | 13:4d5aae46f850 |
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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 ============== |