From fc3c6eef97be5ad42671c8d4f9cf5cbffbbe3b90 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sun, 18 Apr 2021 22:18:14 +0200
Subject: [PATCH 1/6] grep: add option to keep header

https://github.com/galaxyproject/tools-iuc/issues/3511
---
 tools/filters/grep.py  |  9 ++++++++-
 tools/filters/grep.xml | 19 +++++++++++++++++--
 2 files changed, 25 insertions(+), 3 deletions(-)

diff --git a/tools/filters/grep.py b/tools/filters/grep.py
index fad39281aac..15cc6342e94 100644
--- a/tools/filters/grep.py
+++ b/tools/filters/grep.py
@@ -44,6 +44,7 @@ def main():
         print(" -o Output file")
         print(" -pattern RegEx pattern")
         print(" -v true or false (Invert match)")
+        print(" --keep_header true or false (keep header)")
         return 0
 
     outputfile = opts.get("-o")
@@ -66,6 +67,10 @@ def main():
         print("RegEx pattern not specified.")
         return -4
 
+    keep_header = opts.get("--keep_header")
+    if keep_header is None:
+        print("keep header not specified.")
+        return -5
     # All inputs have been specified at this point, now validate.
 
     # replace if input has been escaped, remove sq
@@ -121,7 +126,9 @@ def main():
     open(pattern_file_name, 'w').write(pattern)
 
     # generate grep command
-    commandline = "grep %s %s -f %s %s > %s" % (versionflag, invertflag, pattern_file_name, inputfile, outputfile)
+    if keep_header == "true":
+        commandline = "head -n 1 %s > %s" % (inputfile, outputfile)
+    commandline += "grep %s %s -f %s %s >> %s" % (versionflag, invertflag, pattern_file_name, inputfile, outputfile)
 
     # run grep
     errorcode = subprocess.call(commandline, shell=True)
diff --git a/tools/filters/grep.xml b/tools/filters/grep.xml
index c904bb4c769..f83c2b6bfd1 100644
--- a/tools/filters/grep.xml
+++ b/tools/filters/grep.xml
@@ -1,9 +1,9 @@
-<tool id="Grep1" name="Select" version="1.0.1">
+<tool id="Grep1" name="Select" version="1.0.2">
   <description>lines that match an expression</description>
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>
-  <command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert</command>
+  <command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert --keep_header $keep_header</command>
   <inputs>
     <param format="txt" name="input" type="data" label="Select lines from"/>
     <param name="invert" type="select" label="that">
@@ -20,6 +20,7 @@
         </mapping>
       </sanitizer>
     </param>
+    <param name="keep_header" type="boolean" truevalue="true" falsevalue="false" label="Keep header line" help="i.e. the first line is kept independent of the regular expression"/>
   </inputs>
   <outputs>
     <data format="input" name="out_file1" metadata_source="input"/>
@@ -31,6 +32,20 @@
       <param name="pattern" value="^chr[0-9]*"/>
       <output name="out_file1" file="fs-grep.dat"/>
     </test>
+    <test>
+      <param name="input" value="1.bed"/>
+      <param name="invert" value="false"/>
+      <param name="pattern" value="+"/>
+      <param name="keep_header" value="true"/>
+      <output name="out_file1">
+        <assert_contents>
+          <not_has_text text="CCDS989.1_cds_0_0_chr1_147962193_r"/>
+        </assert_contents>
+      </output>
+    </test>
+    
+    
+    CCDS989.1_cds_0_0_chr1_147962193_r
   </tests>
   <help>
 

From d1e3edfb689229cb689c595cce57bd195ca50775 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 19 Apr 2021 13:57:57 +0200
Subject: [PATCH 2/6] consider header in tail/head wrapper

and remove pl wrapper
---
 tools/filters/headWrapper.pl  | 18 ------------------
 tools/filters/headWrapper.xml | 32 +++++++++++++++++++++++++++++---
 tools/filters/tailWrapper.pl  | 19 -------------------
 tools/filters/tailWrapper.xml | 35 +++++++++++++++++++++++++++++++----
 4 files changed, 60 insertions(+), 44 deletions(-)
 delete mode 100644 tools/filters/headWrapper.pl
 delete mode 100644 tools/filters/tailWrapper.pl

diff --git a/tools/filters/headWrapper.pl b/tools/filters/headWrapper.pl
deleted file mode 100644
index 89aa006fb5a..00000000000
--- a/tools/filters/headWrapper.pl
+++ /dev/null
@@ -1,18 +0,0 @@
-#! /usr/bin/env perl
-
-use strict;
-use warnings;
-
-# a wrapper for head for use in galaxy
-# headWrapper.pl [filename] [# lines to show] [output]
-
-die "Check arguments" unless @ARGV == 3;
-die "Line number must be an integer\n" unless $ARGV[1]=~ m/^\d+$/;
-
-open (OUT, ">$ARGV[2]") or die "Cannot create $ARGV[2]:$!\n";
-open (HEAD, "head -n $ARGV[1] $ARGV[0]|") or die "Cannot run head:$!\n";
-while (<HEAD>) {
-    print OUT;
-}
-close OUT;
-close HEAD;
diff --git a/tools/filters/headWrapper.xml b/tools/filters/headWrapper.xml
index 477f1f77684..fc366042b4a 100644
--- a/tools/filters/headWrapper.xml
+++ b/tools/filters/headWrapper.xml
@@ -4,11 +4,21 @@
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>
   <command>
-perl '$__tool_directory__/headWrapper.pl' '$input' $lineNum '$out_file1'
+    set -eo pipefail;
+    (
+    #if $header
+      head -n 1 '$input' &&
+      tail -n +1 '$input'
+    #else
+      cat '$input'
+    #end if
+    | head -n 1 $lineNum 
+    ) > '$out_file1'
   </command>
   <inputs>
-    <param name="lineNum" type="integer" value="10" label="Select first" help="lines"/>
+    <param name="lineNum" type="integer" value="10" min="1" label="Select first" help="lines"/>
     <param name="input" type="data" format="txt" label="from"/>
+    <param name="header" type="boolean" label="Dataset has a header" help="if checked the header is kept and is not counted as a kept line"/>
   </inputs>
   <outputs>
     <data name="out_file1" format="input" metadata_source="input"/>
@@ -17,7 +27,23 @@ perl '$__tool_directory__/headWrapper.pl' '$input' $lineNum '$out_file1'
     <test>
       <param name="lineNum" value="10"/>
       <param name="input" value="1.bed"/>
-      <output name="out_file1" file="eq-showbeginning.dat"/>
+      <output name="out_file1" file="eq-showbeginning.dat">
+        <assert_contents>
+          <not_has_text text="CCDS9526.1_cds_0_0_chr13_112381695_f"/>
+          <has_n_lines n="10"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="lineNum" value="10"/>
+      <param name="input" value="1.bed"/>
+      <param name="header" value="true"/>
+      <output name="out_file1">
+        <assert_contents>
+          <has_text text="CCDS9526.1_cds_0_0_chr13_112381695_f"/>
+          <has_n_lines n="11"/>
+        </assert_contents>
+      </output>
     </test>
   </tests>
   <help>
diff --git a/tools/filters/tailWrapper.pl b/tools/filters/tailWrapper.pl
deleted file mode 100644
index 35e7d4ee51c..00000000000
--- a/tools/filters/tailWrapper.pl
+++ /dev/null
@@ -1,19 +0,0 @@
-#! /usr/bin/env perl
-
-use strict;
-use warnings;
-
-# a wrapper for tail for use in galaxy
-# lessWrapper.pl [filename] [# lines to show] [output]
-
-die "Check arguments" unless @ARGV == 3;
-die "Line number should be an integer\n" unless $ARGV[1]=~ m/^\d+$/;
-
-open (OUT, ">$ARGV[2]") or die "Cannot create $ARGV[2]:$!\n";
-open (TAIL, "tail -n $ARGV[1] $ARGV[0]|") or die "Cannot run tail:$!\n";
-while (<TAIL>) {
-    print OUT;
-}
-close OUT;
-close TAIL;
-    
diff --git a/tools/filters/tailWrapper.xml b/tools/filters/tailWrapper.xml
index 166018ec1d2..f9fd67adb59 100644
--- a/tools/filters/tailWrapper.xml
+++ b/tools/filters/tailWrapper.xml
@@ -1,10 +1,21 @@
 <tool id="Show tail1" name="Select last" version="1.0.0">
   <description>lines from a dataset</description>
-  <command detect_errors="exit_code">
-perl '$__tool_directory__/tailWrapper.pl' '$input' $lineNum '$out_file1'</command>
+  <command detect_errors="exit_code"><![CDATA[
+    set -eo pipefail;
+    (
+    #if $header
+      head -n 1 '$input' &&
+      tail -n +1 '$input'
+    #else
+      cat '$input'
+    #end if
+    | tail -n $lineNum
+    ) > '$out_file1'
+  ]]></command>
   <inputs>
-    <param name="lineNum" type="integer" value="10" label="Select last" help="lines"/>
+    <param name="lineNum" type="integer" value="10" min="1" label="Select last" help="lines"/>
     <param name="input" type="data" format="txt" label="from"/>
+    <param name="header" type="boolean" label="Dataset has a header" help="if checked the header is kept and is not counted as a kept line"/>
   </inputs>
   <outputs>
     <data name="out_file1" format_source="input" metadata_source="input"/>
@@ -13,7 +24,23 @@ perl '$__tool_directory__/tailWrapper.pl' '$input' $lineNum '$out_file1'</comman
     <test>
       <param name="lineNum" value="10"/>
       <param name="input" value="1.bed"/>
-      <output name="out_file1" file="eq-showtail.dat"/>
+      <output name="out_file1" file="eq-showtail.dat">
+        <assert_contents>
+          <not_has_text text="CCDS989.1_cds_0_0_chr1_147962193_r"/>
+          <has_n_lines n="10"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test>
+      <param name="lineNum" value="10"/>
+      <param name="input" value="1.bed"/>
+      <param name="header" value="true"/>
+      <output name="out_file1">
+        <assert_contents>
+          <has_text text="CCDS989.1_cds_0_0_chr1_147962193_r"/>
+          <has_n_lines n="11"/>
+        </assert_contents>
+      </output>
     </test>
   </tests>
   <help>

From 8cc1c3bc0fb02d8501227336e7525f4ad298c8a5 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 3 May 2021 13:15:08 +0200
Subject: [PATCH 3/6] some updates for grep, tail, head

- CDATA for all
- exit code
- remove interpreter
- bump versions
- and add the tools to WORKFLOW_SAFE_TOOL_VERSION_UPDATES
---
 lib/galaxy/tools/__init__.py  | 3 +++
 tools/filters/grep.xml        | 4 +++-
 tools/filters/headWrapper.xml | 4 ++--
 tools/filters/tailWrapper.xml | 2 +-
 4 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index 058cfb901c8..32e09407a33 100644
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -197,6 +197,9 @@ WORKFLOW_SAFE_TOOL_VERSION_UPDATES = {
     '__BUILD_LIST__': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
     '__APPLY_RULES__': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.1.0")),
     '__EXTRACT_DATASET__': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
+    'Grep1': safe_update(packaging.version.parse("1.0.1"), packaging.version.parse("1.0.2")),
+    'Show beginning1': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
+    'Show tail1': safe_update(packaging.version.parse("1.0.0"), packaging.version.parse("1.0.1")),
 }
 
 
diff --git a/tools/filters/grep.xml b/tools/filters/grep.xml
index f83c2b6bfd1..443036e4dab 100644
--- a/tools/filters/grep.xml
+++ b/tools/filters/grep.xml
@@ -3,7 +3,9 @@
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>
-  <command interpreter="python">grep.py -i $input -o $out_file1 -pattern '$pattern' -v $invert --keep_header $keep_header</command>
+  <command detect_errors="exit_code"><![CDATA[
+    python '$__tool_directory__/grep.py' -i '$input' -o '$out_file1' -pattern '$pattern' -v $invert --keep_header $keep_header
+  ]]></command>
   <inputs>
     <param format="txt" name="input" type="data" label="Select lines from"/>
     <param name="invert" type="select" label="that">
diff --git a/tools/filters/headWrapper.xml b/tools/filters/headWrapper.xml
index fc366042b4a..c3bb077647d 100644
--- a/tools/filters/headWrapper.xml
+++ b/tools/filters/headWrapper.xml
@@ -3,7 +3,7 @@
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>
-  <command>
+  <command detect_errors="exit_code"><![CDATA[
     set -eo pipefail;
     (
     #if $header
@@ -14,7 +14,7 @@
     #end if
     | head -n 1 $lineNum 
     ) > '$out_file1'
-  </command>
+  ]]></command>
   <inputs>
     <param name="lineNum" type="integer" value="10" min="1" label="Select first" help="lines"/>
     <param name="input" type="data" format="txt" label="from"/>
diff --git a/tools/filters/tailWrapper.xml b/tools/filters/tailWrapper.xml
index f9fd67adb59..e37516b5828 100644
--- a/tools/filters/tailWrapper.xml
+++ b/tools/filters/tailWrapper.xml
@@ -1,4 +1,4 @@
-<tool id="Show tail1" name="Select last" version="1.0.0">
+<tool id="Show tail1" name="Select last" version="1.0.1">
   <description>lines from a dataset</description>
   <command detect_errors="exit_code"><![CDATA[
     set -eo pipefail;

From 85f643bc6630731ba810ac0b82c47a0e5ac89553 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 4 May 2021 10:49:23 +0200
Subject: [PATCH 4/6] remove python wrapper for grep tool

and fix cli (`-n +2`) for head, tail, grep
---
 tools/filters/grep.py         | 144 ----------------------------------
 tools/filters/grep.xml        |  40 +++++++---
 tools/filters/headWrapper.xml |  13 ++-
 tools/filters/tailWrapper.xml |   2 +-
 4 files changed, 34 insertions(+), 165 deletions(-)
 delete mode 100644 tools/filters/grep.py

diff --git a/tools/filters/grep.py b/tools/filters/grep.py
deleted file mode 100644
index 15cc6342e94..00000000000
--- a/tools/filters/grep.py
+++ /dev/null
@@ -1,144 +0,0 @@
-# Filename: grep.py
-# Author: Ian N. Schenck
-# Version: 8/23/2005
-#
-# This script accepts regular expressions, as well as an "invert"
-# option, and applies the regular expression using grep.  This wrapper
-# provides security and pipeline.
-#
-# Grep is launched based on these inputs:
-# -i Input file
-# -o Output file
-# -pattern RegEx pattern
-# -v true or false (output NON-matching lines)
-from __future__ import print_function
-
-import os
-import re
-import subprocess
-import sys
-from subprocess import PIPE, Popen
-from tempfile import NamedTemporaryFile
-
-
-# This function is exceedingly useful, perhaps package for reuse?
-def getopts(argv):
-    opts = {}
-    while argv:
-        if argv[0][0] == '-':
-            opts[argv[0]] = argv[1]
-            argv = argv[2:]
-        else:
-            argv = argv[1:]
-    return opts
-
-
-def main():
-    args = sys.argv[1:]
-
-    try:
-        opts = getopts(args)
-    except IndexError:
-        print("Usage:")
-        print(" -i Input file")
-        print(" -o Output file")
-        print(" -pattern RegEx pattern")
-        print(" -v true or false (Invert match)")
-        print(" --keep_header true or false (keep header)")
-        return 0
-
-    outputfile = opts.get("-o")
-    if outputfile is None:
-        print("No output file specified.")
-        return -1
-
-    inputfile = opts.get("-i")
-    if inputfile is None:
-        print("No input file specified.")
-        return -2
-
-    invert = opts.get("-v")
-    if invert is None:
-        print("Match style (Invert or normal) not specified.")
-        return -3
-
-    pattern = opts.get("-pattern")
-    if pattern is None:
-        print("RegEx pattern not specified.")
-        return -4
-
-    keep_header = opts.get("--keep_header")
-    if keep_header is None:
-        print("keep header not specified.")
-        return -5
-    # All inputs have been specified at this point, now validate.
-
-    # replace if input has been escaped, remove sq
-    # characters that are allowed but need to be escaped
-    mapped_chars = {'>': '__gt__',
-                    '<': '__lt__',
-                    '\'': '__sq__',
-                    '"': '__dq__',
-                    '[': '__ob__',
-                    ']': '__cb__',
-                    '{': '__oc__',
-                    '}': '__cc__'}
-
-    # with new sanitizing we only need to replace for single quote,
-    # but this needs to remain for backwards compatibility
-    for key, value in mapped_chars.items():
-        pattern = pattern.replace(value, key)
-
-    # match filename and invert flag
-    fileRegEx = re.compile(r"^[A-Za-z0-9./\-_]+$")
-    invertRegEx = re.compile(r"(true)|(false)")
-
-    # verify that filename and inversion flag are in the correct format
-    if not fileRegEx.match(outputfile):
-        print("Illegal output filename.")
-        return -5
-    if not fileRegEx.match(inputfile):
-        print("Illegal input filename.")
-        return -6
-    if not invertRegEx.match(invert):
-        print("Illegal invert option.")
-        return -7
-
-    # invert grep search?
-    if invert == "true":
-        invertflag = "-v"
-        print("Not matching pattern: %s" % pattern)
-    else:
-        invertflag = ""
-        print("Matching pattern: %s" % pattern)
-
-    # set version flag
-    versionflag = "-P"
-
-    # MacOS 10.8.2 does not support -P option for perl-regex anymore
-    versionmatch = Popen("grep -V | grep 'BSD'", shell=True, stdout=PIPE).communicate()[0]
-    if versionmatch:
-        versionflag = "-E"
-
-    # create temp file holding pattern
-    # by using a file to hold the pattern, we don't have worry about sanitizing grep commandline and can include single quotes in pattern
-    pattern_file_name = NamedTemporaryFile().name
-    open(pattern_file_name, 'w').write(pattern)
-
-    # generate grep command
-    if keep_header == "true":
-        commandline = "head -n 1 %s > %s" % (inputfile, outputfile)
-    commandline += "grep %s %s -f %s %s >> %s" % (versionflag, invertflag, pattern_file_name, inputfile, outputfile)
-
-    # run grep
-    errorcode = subprocess.call(commandline, shell=True)
-
-    # remove temp pattern file
-    os.unlink(pattern_file_name)
-
-    # return error code
-    return errorcode
-
-
-if __name__ == "__main__":
-    main()
diff --git a/tools/filters/grep.xml b/tools/filters/grep.xml
index 443036e4dab..0d26a090a34 100644
--- a/tools/filters/grep.xml
+++ b/tools/filters/grep.xml
@@ -4,39 +4,45 @@
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>
   <command detect_errors="exit_code"><![CDATA[
-    python '$__tool_directory__/grep.py' -i '$input' -o '$out_file1' -pattern '$pattern' -v $invert --keep_header $keep_header
+    set -eo pipefail;
+    #if $keep_header
+      head -n 1 '$input' > '$out_file1' &&
+      tail -n +2 '$input'
+    #else
+      cat '$input'
+    #end if
+    | grep -f '$pattern_file' $invert > '$out_file1'
   ]]></command>
+  <configfiles>
+    <configfile name="pattern_file">$pattern</configfile>
+  </configfiles>
   <inputs>
     <param format="txt" name="input" type="data" label="Select lines from"/>
     <param name="invert" type="select" label="that">
-      <option value="false">Matching</option>
-      <option value="true">NOT Matching</option>
+      <option value="">Matching</option>
+      <option value="-v">NOT Matching</option>
     </param>
     <param name="pattern" type="text" value="^chr([0-9A-Za-z])+" label="the pattern" help="here you can enter text or regular expression (for syntax check lower part of this frame)">
       <sanitizer>
         <valid initial="string.printable">
-         <remove value="&apos;"/>
         </valid>
-        <mapping initial="none">
-          <add source="&apos;" target="__sq__"/>
-        </mapping>
       </sanitizer>
     </param>
     <param name="keep_header" type="boolean" truevalue="true" falsevalue="false" label="Keep header line" help="i.e. the first line is kept independent of the regular expression"/>
   </inputs>
   <outputs>
-    <data format="input" name="out_file1" metadata_source="input"/>
+    <data format_source="input" name="out_file1" metadata_source="input"/>
   </outputs>
   <tests>
     <test>
       <param name="input" value="1.bed"/>
-      <param name="invert" value="false"/>
+      <param name="invert" value=""/>
       <param name="pattern" value="^chr[0-9]*"/>
       <output name="out_file1" file="fs-grep.dat"/>
     </test>
     <test>
       <param name="input" value="1.bed"/>
-      <param name="invert" value="false"/>
+      <param name="invert" value=""/>
       <param name="pattern" value="+"/>
       <param name="keep_header" value="true"/>
       <output name="out_file1">
@@ -45,9 +51,17 @@
         </assert_contents>
       </output>
     </test>
-    
-    
-    CCDS989.1_cds_0_0_chr1_147962193_r
+    <test>
+      <param name="input" value="1.bed"/>
+      <param name="invert" value=""/>
+      <param name="pattern" value="&lt;&gt;\&quot;[]{}"/>
+      <param name="keep_header" value="true"/>
+      <output name="out_file1">
+        <assert_contents>
+          <not_has_text text="CCDS989.1_cds_0_0_chr1_147962193_r"/>
+        </assert_contents>
+      </output>
+    </test>
   </tests>
   <help>
 
diff --git a/tools/filters/headWrapper.xml b/tools/filters/headWrapper.xml
index c3bb077647d..0b20f766207 100644
--- a/tools/filters/headWrapper.xml
+++ b/tools/filters/headWrapper.xml
@@ -1,19 +1,18 @@
-<tool id="Show beginning1" name="Select first" version="1.0.0">
+<tool id="Show beginning1" name="Select first" version="1.0.1">
   <description>lines from a dataset</description>
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>
   <command detect_errors="exit_code"><![CDATA[
     set -eo pipefail;
-    (
     #if $header
-      head -n 1 '$input' &&
-      tail -n +1 '$input'
+      head -n 1 '$input' > '$out_file1' &&
+      tail -n +2 '$input'
     #else
       cat '$input'
     #end if
-    | head -n 1 $lineNum 
-    ) > '$out_file1'
+    | head -n $lineNum 
+    >> '$out_file1'
   ]]></command>
   <inputs>
     <param name="lineNum" type="integer" value="10" min="1" label="Select first" help="lines"/>
@@ -21,7 +20,7 @@
     <param name="header" type="boolean" label="Dataset has a header" help="if checked the header is kept and is not counted as a kept line"/>
   </inputs>
   <outputs>
-    <data name="out_file1" format="input" metadata_source="input"/>
+    <data name="out_file1" format_source="input" metadata_source="input"/>
   </outputs>
   <tests>
     <test>
diff --git a/tools/filters/tailWrapper.xml b/tools/filters/tailWrapper.xml
index e37516b5828..fcf20fa43b9 100644
--- a/tools/filters/tailWrapper.xml
+++ b/tools/filters/tailWrapper.xml
@@ -5,7 +5,7 @@
     (
     #if $header
       head -n 1 '$input' &&
-      tail -n +1 '$input'
+      tail -n +2 '$input'
     #else
       cat '$input'
     #end if

From 181b862250b03be41742ec802a7b083551bfc971 Mon Sep 17 00:00:00 2001
From: M Bernt <m.bernt@ufz.de>
Date: Tue, 4 May 2021 13:47:29 +0200
Subject: [PATCH 5/6] Apply suggestions from code review

- add profile
- add requirement

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
---
 tools/filters/grep.xml        | 5 ++++-
 tools/filters/headWrapper.xml | 5 ++++-
 tools/filters/tailWrapper.xml | 5 ++++-
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/tools/filters/grep.xml b/tools/filters/grep.xml
index 0d26a090a34..d94fc62677e 100644
--- a/tools/filters/grep.xml
+++ b/tools/filters/grep.xml
@@ -1,4 +1,7 @@
-<tool id="Grep1" name="Select" version="1.0.2">
+<tool id="Grep1" name="Select" version="1.0.2" profile="20.05">
+  <requirements>
+    <requirement type="package" version="3.4">grep</requirement>
+  </requirements>
   <description>lines that match an expression</description>
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
diff --git a/tools/filters/headWrapper.xml b/tools/filters/headWrapper.xml
index 0b20f766207..30776b148ac 100644
--- a/tools/filters/headWrapper.xml
+++ b/tools/filters/headWrapper.xml
@@ -1,8 +1,11 @@
-<tool id="Show beginning1" name="Select first" version="1.0.1">
+<tool id="Show beginning1" name="Select first" version="1.0.1" profile="20.05">
   <description>lines from a dataset</description>
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>
+  <requirements>
+    <requirement type="package" version="8.31">coreutils</requirement>
+  </requirements>
   <command detect_errors="exit_code"><![CDATA[
     set -eo pipefail;
     #if $header
diff --git a/tools/filters/tailWrapper.xml b/tools/filters/tailWrapper.xml
index fcf20fa43b9..b1b59bcc419 100644
--- a/tools/filters/tailWrapper.xml
+++ b/tools/filters/tailWrapper.xml
@@ -1,5 +1,8 @@
-<tool id="Show tail1" name="Select last" version="1.0.1">
+<tool id="Show tail1" name="Select last" version="1.0.1" profile="20.05">
   <description>lines from a dataset</description>
+  <requirements>
+    <requirement type="package" version="8.31">coreutils</requirement>
+  </requirements>
   <command detect_errors="exit_code"><![CDATA[
     set -eo pipefail;
     (

From a45f06b8819e2dcc130c02044f1e3fed7e60ffd0 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 4 May 2021 14:59:23 +0200
Subject: [PATCH 6/6] fix test 3 and error detection

only error for exit code > 1:
---
 tools/filters/grep.xml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tools/filters/grep.xml b/tools/filters/grep.xml
index 0d26a090a34..b2ff78cbc34 100644
--- a/tools/filters/grep.xml
+++ b/tools/filters/grep.xml
@@ -3,7 +3,10 @@
   <edam_operations>
     <edam_operation>operation_3695</edam_operation>
   </edam_operations>
-  <command detect_errors="exit_code"><![CDATA[
+  <stdio>
+    <exit_code range="2:" level="warning" description="Select failed" />
+  </stdio>
+  <command><![CDATA[
     set -eo pipefail;
     #if $keep_header
       head -n 1 '$input' > '$out_file1' &&
@@ -54,7 +57,7 @@
     <test>
       <param name="input" value="1.bed"/>
       <param name="invert" value=""/>
-      <param name="pattern" value="&lt;&gt;\&quot;[]{}"/>
+      <param name="pattern" value="&lt;&gt;\&quot;[A]{1}"/>
       <param name="keep_header" value="true"/>
       <output name="out_file1">
         <assert_contents>