# HG changeset patch
# User bgruening
# Date 1741380260 0
# Node ID 3dc70b59608c81e1e5b4602d721f128026f0f855
# Parent  86755160afbf2b7bb35a227c315612baa67089ce
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/text_processing commit 2dc2df988bd2dde9f8d7f629b594186dbd4fdc2b

diff -r 86755160afbf -r 3dc70b59608c awk.xml
--- a/awk.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/awk.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="creator"/>
     <requirements>
-        <requirement type="package" version="5.3.0">gawk</requirement>
+        <requirement type="package" version="5.3.1">gawk</requirement>
     </requirements>
     <version_command>awk --version | head -n 1</version_command>
     <command>
diff -r 86755160afbf -r 3dc70b59608c cut.xml
--- a/cut.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/cut.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="tp_cut_tool" name="Advanced Cut" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
+<tool id="tp_cut_tool" name="Advanced Cut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>columns from a table (cut)</description>
     <macros>
         <import>macros.xml</import>
@@ -191,14 +191,19 @@
     <tests>
         <test expect_num_outputs="1">
             <param name="input" value="cut1.txt"/>
-            <param name="list" value="1,3,4"/>
-            <param name="delimiter" value=""/>
+            <conditional name="cut_type_options">
+                <param name="cut_element" value="-f"/>
+                <param name="delimiter" value="" />
+                 <conditional name="colnames_option">
+                    <param name="header" value="Y"/>
+                    <param name="list" value="1,3,4"/>
+                </conditional>
+            </conditional>
             <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">
@@ -217,9 +222,10 @@
         </test>
         <test expect_num_outputs="1">
             <param name="input" value="cut1.txt"/>
-            <param name="list" value="-3" />
-            <param name="delimiter" value="" />
-            <param name="cut_element" value="-c" />
+            <conditional name="cut_type_options">
+                <param name="cut_element" value="-c" />
+                <param name="list" value="-3" />
+            </conditional>
             <output name="output" file="cut_results3.txt"/>
         </test>
     </tests>
diff -r 86755160afbf -r 3dc70b59608c grep.xml
--- a/grep.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/grep.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -85,7 +85,7 @@
         <!-- grep a FASTA file for sequences with specific motif -->
         <test>
             <param name="infile" value="grep1.txt" />
-            <param name="case_sensitive" value="case sensitive" />
+            <param name="case_sensitive" value="-i" />
             <param name="regex_type" value="-P" />
             <param name="invert" value="" />
             <param name="url_paste" value="AA.{2}GT" />
@@ -98,7 +98,7 @@
              show highlighed output -->
         <test>
             <param name="infile" value="grep1.txt" />
-            <param name="case_sensitive" value="case sensitive" />
+            <param name="case_sensitive" value="-i" />
             <param name="regex_type" value="-P" />
             <param name="invert" value="" />
             <param name="url_paste" value="AA.{2}GT" />
@@ -110,7 +110,7 @@
         <!-- tests egrep -->
         <test>
             <param name="infile" value="egrep1.txt" />
-            <param name="case_sensitive" value="case sensitive" />
+            <param name="case_sensitive" value="-i" />
             <param name="regex_type" value="-E" />
             <param name="invert" value="" />
             <param name="url_paste" value="[^ ]+" />
@@ -122,7 +122,7 @@
         <!-- tests basic regex; + must be backslashed to match -->
         <test>
             <param name="infile" value="egrep1.txt" />
-            <param name="case_sensitive" value="case sensitive" />
+            <param name="case_sensitive" value="-i" />
             <param name="regex_type" value="-G" />
             <param name="invert" value="" />
             <param name="url_paste" value="[^ ]\+" />
@@ -134,7 +134,7 @@
         <!-- tests regex;matching nothing -->
         <test>
             <param name="infile" value="egrep1.txt" />
-            <param name="case_sensitive" value="case sensitive" />
+            <param name="case_sensitive" value="-i" />
             <param name="regex_type" value="-G" />
             <param name="invert" value="" />
             <param name="url_paste" value="not existent pattern" />
@@ -150,7 +150,7 @@
         <!-- tests invalid regex; i.e. that we still get exit code 2 -->
         <test expect_failure="true" expect_exit_code="2">
             <param name="infile" value="egrep1.txt" />
-            <param name="case_sensitive" value="case sensitive" />
+            <param name="case_sensitive" value="-i" />
             <param name="regex_type" value="-G" />
             <param name="invert" value="" />
             <param name="url_paste" value="\(" />
diff -r 86755160afbf -r 3dc70b59608c macros.xml
--- a/macros.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/macros.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -1,12 +1,12 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="9.3">coreutils</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">coreutils</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@TOOL_VERSION@">9.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">9.5</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">23.1</token>
     <xml name="stdio">
         <stdio>
diff -r 86755160afbf -r 3dc70b59608c multijoin.xml
--- a/multijoin.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/multijoin.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -52,7 +52,7 @@
             <param name="first_file" value="multijoin1.txt" />
             <param name="files" value="multijoin2.txt,multijoin3.txt" />
             <param name="key_column" value="4" />
-            <param name="value_columns" value="c7,c8,c9" />
+            <param name="value_columns" value="7,8,9" />
             <param name="output_header" value="True" />
             <output name="outfile" file="multijoin_result1.txt" lines_diff="2" />
         </test>
diff -r 86755160afbf -r 3dc70b59608c recurring_lines.xml
--- a/recurring_lines.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/recurring_lines.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -44,21 +44,27 @@
         <test>
             <repeat name="token_set">
                 <param name="line" value="freedom" />
-                <param name="repeat_select_opts" value="file" />
-                <param name="infile" value="multijoin2.txt" />
+                <conditional name="repeat_select">
+                    <param name="repeat_select_opts" value="file" />
+                    <param name="infile" value="multijoin2.txt" />
+                </conditional>
             </repeat>
             <output name="outfile" file="recurring_result1.txt" />
         </test>
         <test>
             <repeat name="token_set">
                 <param name="line" value="freedom" />
-                <param name="repeat_select_opts" value="user" />
-                <param name="times" value="10" />
+                <conditional name="repeat_select">
+                    <param name="repeat_select_opts" value="user" />
+                    <param name="times" value="10" />
+                </conditional>
             </repeat>
             <repeat name="token_set">
                 <param name="line" value="war is over" />
-                <param name="repeat_select_opts" value="user" />
-                <param name="times" value="10" />
+                <conditional name="repeat_select">
+                    <param name="repeat_select_opts" value="user" />
+                    <param name="times" value="10" />
+                </conditional>
             </repeat>
             <output name="outfile" file="recurring_result2.txt" />
         </test>
diff -r 86755160afbf -r 3dc70b59608c replace_text_in_column.xml
--- a/replace_text_in_column.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/replace_text_in_column.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -5,7 +5,7 @@
     </macros>
     <expand macro="creator"/>
     <requirements>
-        <requirement type="package" version="5.3.0">gawk</requirement>
+        <requirement type="package" version="5.3.1">gawk</requirement>
     </requirements>
     <version_command>awk --version | head -n 1</version_command>
     <command>
@@ -51,9 +51,11 @@
     <tests>
         <test>
               <param name="infile" value="replace_text_in_column1.txt" ftype="tabular" />
-              <param name="column" value="4" />
-              <param name="find_pattern" value=".+_(R.)" />
-              <param name="replace_pattern" value="\\1" />
+              <repeat name="replacements">
+                <param name="column" value="4" />
+                <param name="find_pattern" value=".+_(R.)" />
+                <param name="replace_pattern" value="\\1" />
+              </repeat>
               <output name="outfile" file="replace_text_in_column_results1.txt" />
         </test>
         <test>
diff -r 86755160afbf -r 3dc70b59608c replace_text_in_line.xml
--- a/replace_text_in_line.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/replace_text_in_line.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -14,6 +14,7 @@
       -r
       --sandbox
       #for $replacement in $replacements:
+        -e '$replacement.sed_options'
         -e
         's/$replacement.find_pattern/$replacement.replace_pattern/g'
       #end for
@@ -47,10 +48,20 @@
                     <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />
                     <add source="/" target="\/"/>
                 </mapping>
-
             </sanitizer>
-
-        </param>
+         </param>
+         <param name="sed_options" type="text" size="20" optional="true" label="Additional sed commands before replacement" help="Provide additional sed commands before the replacement (e.g., ':a;N;$!ba;')." >
+            <sanitizer>
+              <valid initial="string.printable">
+                  <remove value="&#39;"/>  <!-- Removes single quotes -->
+                  <remove value="/"/>     <!-- Removes slashes -->
+              </valid>
+              <mapping initial="none">
+                  <add source="&#39;" target="&#39;&quot;&#39;&quot;&#39;" />  <!-- Escapes single quotes -->
+                  <add source="/" target="\/"/>                         <!-- Escapes slashes -->
+              </mapping>
+            </sanitizer>
+         </param>
       </repeat>
     </inputs>
     <outputs>
@@ -59,8 +70,11 @@
     <tests>
          <test>
             <param name="infile" value="replace_text_in_line1.txt" />
-            <param name="find_pattern" value="CTC." />
-            <param name="replace_pattern" value="FOOBAR" />
+            <repeat name="replacements">
+              <param name="find_pattern" value="CTC." />
+              <param name="replace_pattern" value="FOOBAR" />
+              <param name="sed_options" value="" />
+            </repeat>
             <output name="outfile" file="replace_text_in_line_results1.txt" />
         </test>
         <test>
@@ -68,13 +82,24 @@
             <repeat name="replacements">
               <param name="find_pattern" value="CTC." />
               <param name="replace_pattern" value="FOOBAR" />
+              <param name="sed_options" value="" />
             </repeat>
             <repeat name="replacements">
               <param name="find_pattern" value="chr" />
               <param name="replace_pattern" value="domain" />
+              <param name="sed_options" value="" />
             </repeat>
             <output name="outfile" file="replace_text_in_line_results2.txt" />
         </test>
+        <test>
+            <param name="infile" value="replace_text_in_line1.txt" />
+            <repeat name="replacements">
+            <param name="find_pattern" value="\n" />
+            <param name="replace_pattern" value="" />
+            <param name="sed_options" value=":a;N;$!ba" />
+            </repeat>
+            <output name="outfile" file="replace_text_in_line_results3.txt" />
+        </test>
     </tests>
     <help>
 <![CDATA[
@@ -155,7 +180,9 @@
 - **\|** Separates alternate possibilities.
 
 
-**Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported.
+**Note**: SED uses extended regular expression syntax, not Perl syntax. **\\d**, **\\w**, **\\s** etc. are **not** supported. However, you can use SED FAQ to perform commands using special characters.
+        More complex options can look like `sed -e '$!N;s/foo/bar/;'`. Here, `$!N;` is an optional part which you only need to set in very special cases. The `foo` part is the search string, and the `bar` part is the replacement string.
+        Please read the SED FAQ here: https://www.pement.org/sed/sedfaq3.html#s3.2
 
 ]]>
     </help>
diff -r 86755160afbf -r 3dc70b59608c sed.xml
--- a/sed.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/sed.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -56,14 +56,19 @@
         <test>
             <param name="infile" value="sed1.txt" />
             <param name="code" value="1d ; s/foo/bar/" />
-            <param name="silent" value="" />
+            <conditional name="adv_opts">
+                <param name="adv_opts_selector" value="advanced" />
+                <param name="silent" value="" />
+            </conditional>
             <output name="output" file="sed_results1.txt" />
         </test>
         <test>
             <param name="infile" value="sed1.txt" />
             <param name="code" value="/foo/ { s/foo/baz/g ; p }" />
-            <param name="adv_opts_selector" value="advanced" />
-            <param name="silent" value="-n" />
+            <conditional name="adv_opts">
+                <param name="adv_opts_selector" value="advanced" />
+                <param name="silent" value="-n" />
+            </conditional>
             <output name="output" file="sed_results2.txt" />
         </test>
     </tests>
diff -r 86755160afbf -r 3dc70b59608c sort.xml
--- a/sort.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/sort.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -11,7 +11,7 @@
     <command>
 <![CDATA[
         (
-            LC_ALL=C
+            LC_ALL=C;
             #if int($header) > 0:
                 sed -u '${header}'q &&
             #end if
diff -r 86755160afbf -r 3dc70b59608c sorted_uniq.xml
--- a/sorted_uniq.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/sorted_uniq.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -74,17 +74,21 @@
     <tests>
         <test>
             <param name="infile" value="sorted_uniq1.tabular" />
-            <param name="grouping_select" value="no"/>
-            <param name="count" value="True"/>
+            <conditional name="grouping">
+                <param name="grouping_select" value="no"/>
+                <param name="count" value="True"/>
+                <param name="uniqueonly" value="True"/>
+            </conditional>
             <param name="ignorecase" value="True"/>
-            <param name="uniqueonly" value="True"/>
             <output name="outfile" file="sorted_uniq_results1.tabular" />
         </test>
         <test>
             <param name="infile" value="sorted_uniq1.tabular" />
             <param name="ignorecase" value="True"/>
-            <param name="grouping_select" value="yes"/>
-            <param name="group" value="separate"/>
+            <conditional name="grouping">
+                <param name="grouping_select" value="yes"/>
+                <param name="group" value="separate"/>
+            </conditional>
             <output name="outfile" file="sorted_uniq_results2.tabular" />
         </test>
     </tests>
diff -r 86755160afbf -r 3dc70b59608c tac.xml
--- a/tac.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/tac.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -48,8 +48,10 @@
         </test>
         <test>
             <param name="infile" value="1.bed"/>
-            <param name="separator_select" value="yes"/>
-            <param name="before" value="True"/>
+            <conditional name="separator">
+                <param name="separator_select" value="yes"/>
+                <param name="before" value="True"/>
+            </conditional>
             <output name="outfile" file="tac_result2.txt"/>
         </test>
     </tests>
diff -r 86755160afbf -r 3dc70b59608c test-data/recurring_result1.txt
--- a/test-data/recurring_result1.txt	Fri Aug 16 10:41:54 2024 +0000
+++ b/test-data/recurring_result1.txt	Fri Mar 07 20:44:20 2025 +0000
@@ -7,4 +7,3 @@
 freedom
 freedom
 freedom
-freedom
diff -r 86755160afbf -r 3dc70b59608c test-data/replace_text_in_line_results3.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/replace_text_in_line_results3.txt	Fri Mar 07 20:44:20 2025 +0000
@@ -0,0 +1,1 @@
+chr7	56632	56652	D17003_CTCF_R6	310	+chr7	56736	56756	D17003_CTCF_R7	354	+chr7	56761	56781	D17003_CTCF_R4	220	+
diff -r 86755160afbf -r 3dc70b59608c unsorted_uniq.xml
--- a/unsorted_uniq.xml	Fri Aug 16 10:41:54 2024 +0000
+++ b/unsorted_uniq.xml	Fri Mar 07 20:44:20 2025 +0000
@@ -45,9 +45,11 @@
             <param name="infile" value="1.bed"/>
             <param name="is_numeric" value="True"/>
             <param name="ignore_case" value="True"/>
-            <param name="adv_opts_selector" value="advanced"/>
-            <param name="column_start" value="2"/>
-            <param name="column_end" value="3"/>
+            <conditional name="adv_opts">
+                <param name="adv_opts_selector" value="advanced"/>
+                <param name="column_start" value="2"/>
+                <param name="column_end" value="3"/>
+            </conditional>
             <output name="outfile" file="unique_results1.bed"/>
         </test>
     </tests>