Merge pull request #713 from RECETOX/hechth/issue709

fix table tools lint errors

Author: hechth

tools/tables/macros.xml

@@ -28,27 +28,17 @@
 
     <xml name="regex_sanitizer">
         <sanitizer>
-            <valid initial="string.ascii_letters,string.digits">
+            <valid initial="default">
                 <add value="^"/>
                 <add value="$"/>
-                <add value="("/>
-                <add value=")"/>
                 <add value="|"/>
-                <add value="?"/>
-                <add value="*"/>
-                <add value="+"/>
                 <add value="{"/>
                 <add value="}"/>
                 <add value="\"/>
                 <add value="["/>
                 <add value="]"/>
-                <add value="."/>
-                <add value=","/>
-                <add value="_"/>
-                <add value="-"/>
             </valid>
         </sanitizer>
-        <validator type="empty_field" />
         <validator type="regex" message="Pattern must not end with backslash.">.*[^\\]$</validator>
     </xml>
 </macros>

tools/tables/table_pandas_rename_column.xml

@@ -5,7 +5,7 @@
     </xrefs> -->
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <!-- TODO: please annotate this tool with topics and operations from http://edamontology.org -->
     <!-- TODO: for more information see: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html#edam-topics-and-operations -->
@@ -54,8 +54,10 @@
     <tests>
         <test>
             <param name="input_dataset" value="reference.txt" ftype="tabular"/>
-            <param name="column" value="2"/>
-            <param name="new_name" value="retention_time"/>
+            <repeat name="columns_selection">
+                <param name="column" value="2"/>
+                <param name="new_name" value="retention_time"/>
+            </repeat>
             <output name="output_dataset" file="rename/reference_rt_renamed.tabular" ftype="tabular"/>
         </test>
         <test>

tools/tables/table_pandas_rename_columns_regex.xml

@@ -2,7 +2,7 @@
     <description>rename columns in a table using regex</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
 
     <requirements>
@@ -48,11 +48,11 @@
         <test expect_num_outputs="1">
             <param name="input_dataset" value="rename/reference_both_renamed.tabular" ftype="tabular"/>
             <param name="columns" value="1,2"/>
-            <param name="regex_check" value="retention_"/>
-            <param name="regex_replace" value=""/>
+            <param name="regex_check" value="(retention_){1}"/>
             <output name="output_dataset" ftype="tabular">
                 <assert_contents>
 					<has_text text="retention" negate="true"/>
+                    <has_line line="index&#9;time"/>
                 </assert_contents>
             </output>
         </test>