Merge pull request bgruening#1448 from bernt-matthias/topic/fix-cut

Fix cut tool
planemo-autoupdate · Aug 16, 2024 · c2b1677 · c2b1677
2 parents d9c5127 + 4973502
commit c2b1677
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Showing 2 changed files with 9 additions and 3 deletions.
diff --git a/tools/text_processing/text_processing/cut.xml b/tools/text_processing/text_processing/cut.xml
@@ -1,4 +1,4 @@
-<tool id="tp_cut_tool" name="Advanced Cut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="tp_cut_tool" name="Advanced Cut" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>columns from a table (cut)</description>
     <macros>
         <import>macros.xml</import>
@@ -13,10 +13,10 @@
             #if $cut_type_options.cut_element != '-f'
                 '$cut_type_options.list'
             #else
+                '$cut_type_options.colnames_option.list'
                 #if str($cut_type_options.delimiter) != '':
                     -d"$cut_type_options.delimiter"
                 #end if
-                '$cut_type_options.colnames_option.list'
             #end if
             '$input'
         > '$output'
@@ -194,7 +194,11 @@
             <param name="list" value="1,3,4"/>
             <param name="delimiter" value=""/>
             <output name="output" file="cut_results1.txt"/>
+            <assert_command>
+                <has_text text="-f '1,3,4'"/>
+            </assert_command>
         </test>
+
         <test expect_num_outputs="1">
             <param name="input" value="cut1.txt"/>
             <conditional name="cut_type_options">
@@ -207,6 +211,9 @@
             </conditional>
             <param name="complement" value="--complement" />
             <output name="output" file="cut_results2.txt"/>
+            <assert_command>
+                <has_text text="-f '2'"/>
+            </assert_command>
         </test>
         <test expect_num_outputs="1">
             <param name="input" value="cut1.txt"/>

diff --git a/tools/text_processing/text_processing/sort_rows.xml b/tools/text_processing/text_processing/sort_rows.xml
@@ -18,7 +18,6 @@
     <outputs>
         <data name="outfile" format_source="infile" metadata_source="infile"/>
     </outputs>
-    <options sanitize="False"/>
     <tests>
         <test>
             <param name="infile" value="sort_rows1.tabular" ftype="tabular" />