Mercurial > repos > jjohnson > query_tabular

diff filter_tabular.xml @ 21:357fe86f245d draft

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Uploaded
author jjohnson
date Fri, 14 Jul 2017 17:34:22 -0400
parents ab27c4bd14b9
children bed5018e7ae3
line wrap: on
line diff
--- a/filter_tabular.xml	Fri Jul 14 11:39:27 2017 -0400
+++ b/filter_tabular.xml	Fri Jul 14 17:34:22 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="filter_tabular" name="Filter Tabular" version="5.0.0">
+<tool id="filter_tabular" name="Filter Tabular" version="1.0.0">
     <description></description>
 
     <macros>
@@ -7,11 +7,8 @@
 
     <requirements>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
-        python $__tool_directory__/filter_tabular.py 
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/filter_tabular.py'
         -i '$input'
         -j '$filter_json'
         -o '$output'
@@ -36,41 +33,72 @@
         <test>
             <param name="input" ftype="tabular" value="pets.tsv"/>
             <repeat name="linefilters">
-                <param name="filter_type" value="comment"/>
-                <param name="comment_char" value="35"/>
+                <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">
-                <param name="filter_type" value="append_line_num"/>
+                <conditional name="filter">
+                    <param name="filter_type" value="append_line_num"/>
+                </conditional>
             </repeat>
             <repeat name="linefilters">
-                <param name="filter_type" value="select_columns"/>
-                <param name="columns" value="7,2,3,4,1"/>
+                <conditional name="filter">
+                    <param name="filter_type" value="select_columns"/>
+                    <param name="columns" value="7,2,3,4,1"/>
+                </conditional>
             </repeat>
             <repeat name="linefilters">
-                <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 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">
-                <param name="filter_type" value="comment"/>
-                <param name="comment_char" value="35"/>
+                <conditional name="filter">
+                    <param name="filter_type" value="comment"/>
+                    <param name="comment_char" value="35"/>
+                </conditional>
             </repeat>
             <repeat name="linefilters">
-                <param name="filter_type" value="append_line_num"/>
+                <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">
-                <param name="filter_type" value="select_columns"/>
-                <param name="columns" value="c7,c5,c6"/>
+                <conditional name="filter">
+                    <param name="filter_type" value="select_columns"/>
+                    <param name="columns" value="c7,c5,c6"/>
+                </conditional>
             </repeat>
             <repeat name="linefilters">
-                <param name="filter_type" value="normalize"/>
-                <param name="columns" value="c2,c3"/>
-                <param name="separator" value=","/>
+                <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>