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Co-authored-by: Björn Grüning <[email protected]>

Author: nsoranzo

tools/condense_characters/condense_characters.xml

@@ -1,10 +1,16 @@
-<tool id="Condense characters1" name="Condense"  version="1.0.1">
+<tool id="Condense characters1" name="Condense"  version="1.0.1" profile="24.0">
     <description>consecutive characters</description>
+    <requirements>
+        <requirement type="package" version="5.32">perl</requirement>
+    </requirements>
+    <required_files>
+        <include path="condense_characters.pl" />
+    </required_files>
     <command>
-        perl $__tool_directory__/condense_characters.pl
-            "${input}"
-            "${character}"
-            "${out_file1}"
+perl '$__tool_directory__/condense_characters.pl'
+'${input}'
+${character}
+'${out_file1}'
     </command>
     <inputs>
     <!--    <display>condense all consecutive $character from $input</display> -->
@@ -30,7 +36,6 @@
         </test>
     </tests>
     <help>
-
 **What it does**
 
 This tool condenses all consecutive characters of a specified type.

tools/cummerbund/cummeRbund.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy0">
+<tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy0" profile="24.0">
     <description>visualize Cuffdiff output</description>
     <macros>
         <import>cummeRbund_macros.xml</import>
@@ -10,6 +10,9 @@
         <requirement type="package" version="3.5.1">r-base</requirement>
         <requirement type="package" version="@TOOL_VERSION@">bioconductor-cummerbund</requirement>
     </requirements>
+    <required_files>
+        <include path="cummeRbund.R" />
+    </required_files>
     <code file="cummeRbund_options.py"/>
     <command detect_errors="aggressive">
 <![CDATA[

tools/remove_beginning/remove_beginning.xml

@@ -1,13 +1,19 @@
-<tool id="Remove beginning1" name="Remove beginning" version="1.0.1">
+<tool id="Remove beginning1" name="Remove beginning" version="1.0.1" profile="24.0">
     <description>of a file</description>
+    <requirements>
+        <requirement type="package" version="5.32">perl</requirement>
+    </requirements>
+    <required_files>
+        <include path="remove_beginning.pl" />
+    </required_files>
     <command>
-        perl $__tool_directory__/remove_beginning.pl
-            "${input}"
-            "${num_lines}"
-            "${out_file1}"
+perl '$__tool_directory__/remove_beginning.pl'
+'${input}'
+${num_lines}
+'${out_file1}'
     </command>
     <inputs>
-        <param name="num_lines" type="integer" value="1" label="Remove first" help="lines"/>
+        <param name="num_lines" type="integer" min="0" value="1" label="Remove these number of lines from the top"/>
         <param format="txt" name="input" type="data" label="from"/>
     </inputs>
     <outputs>