--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/removeChar.xml	Fri Sep 17 19:29:45 2021 +0000
@@ -0,0 +1,46 @@
+<tool id="removechar" name="removeChar tool" version="1.0.0">
+  <description>allows to remove positions (or columns) from a multi-Fasta alignment file in function of a given character</description>
+
+<!--<requirements>
+  <requirement type="package" version="1.7.2">perl-bioperl</requirement>
+</requirements>-->
+
+<command detect_errors="aggressive"><![CDATA[
+
+#import re
+        ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
+        ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
+            ## Add single quotes around each input file identifier
+            #set $_input_file = "'{}'".format($input.element_identifier)
+            ln -s '${input}' ${_input_file} &&
+
+
+        perl '$__tool_directory__/removeChar.pl' $_input_file $char > "$output"
+
+
+
+]]></command>
+ <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output"  -->
+ <!-- ./nuclescore.sh ${named_input_files} > "$output" -->
+
+<inputs>
+  <param format="fasta" name="input" type="data" label="Multi-FASTA file: "/>
+  <param name="char" type="text" area="false" value="N" label="Character to be removed from Multi-FASTA file:" help="Users can directly write the character to be removed without quotes ("" or '')" />
+</inputs>
+
+ <outputs>
+    <data format="fasta" name="output" />
+ </outputs>
+
+<help><![CDATA[
+removeChar.pl is a Perl script allowing to remove positions (or columns) of an aligned multi-Fasta file in function of a given character (eg. N).
+The resulting multi-Fasta file corresponds to the same input multiFasta alignment file without the queried character.
+
+This script belongs to the getSequenceInfo supplementary tools.
+
+- GitHub: https://github.com/karubiotools/getSequenceInfo/tree/master/supplementary_tools
+]]>
+</help>
+
+</tool>
+