--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/catchsequence/catchsequence.xml	Thu Aug 26 13:41:33 2021 +0000
@@ -0,0 +1,46 @@
+<tool id="catchsequence" name="Catch Sequence" version="0.1.0">
+  <description>Catch sequence for BioloMICS import</description>
+<requirements>
+  <requirement type="package" version="1.0.1">abricate</requirement>
+  <requirement type="package" version="2.19.0">mlst</requirement>
+  <!--<requirement type="package" version="6.6.0">emboss</requirement>
+  <requirement type="package" version="1.3.2">pandas</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')
+        #set $named_input_files = ''
+        #for $input_file in $input_files
+            ## Add single quotes around each input file identifier
+            #set $_input_file = "'{}'".format($input_file.element_identifier)
+            ln -s '${input_file}' ${_input_file} && 
+            #set $named_input_files = $named_input_files + ' ' + $_input_file
+        #end for
+
+	
+  	perl '$__tool_directory__/catchsequence.pl' $named_input_files > "$output"
+	
+       
+
+]]></command>
+ <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output"  -->
+ <!-- ./nuclescore.sh ${named_input_files} > "$output" -->
+
+<inputs>
+  <param type="data" name="input_files" format="fasta" multiple="true" label="Genome fasta files"/>
+  <!-- <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/> -->
+</inputs>
+
+ <outputs>
+    <data format="tabular" name="output" />
+ </outputs>
+
+<help>
+No documentation
+  </help>
+
+</tool>