--- a/kleborate.xml	Tue Jan 11 16:09:59 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-<tool id="kleboratetool" name="Kleborate" version="0.1.0">
-  <description> a tool to screen genome assemblies of Klebsiella pneumoniae</description>
-  <requirements>
-    <requirement type="package" version="2.1.0">kleborate</requirement>
-    <requirement type="package" version="2.0.0">kaptive</requirement>
-  </requirements>
-
-  <!--  kleborateold -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output  
-  /home/linuxipg/Kleborate/kleborate-runner.py -->
-  <command detect_errors="aggressive"><![CDATA[
-       ## 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
-
-        kleborate $r $kaptive_k $kaptive_o -o $output --min_identity $ident --min_coverage $cov -a $named_input_files 
-]]></command>
- 
-  <inputs>
-  <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/>
- 
-  <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):">
-            <option value="">no</option>
-            <option value="-r">yes</option>
-          </param>
-
-          <param name="kaptive_k" type="select" label="Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci):">
-            <option value="">no</option>
-            <option value="--kaptive_k">yes</option>
-          </param>
-
-          <param name="kaptive_o" type="select" label="Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci):">
-            <option value="">no</option>
-            <option value="--kaptive_o">yes</option>
-          </param>
-
-         <param name="ident" type="text" area="false" value="90.0" label="Minimum alignment percent identity for main results:"/> 
-         <param name="cov" type="text" area="false" value="80.0" label="Minimum alignment percent coverage for main results:"/>
-   
- </inputs>
-
- <outputs>  
-    <data format="tabular" name="output" />
- </outputs>
-
- <tests>
-    <test>
-    <param name="input" value="KP011_S63.scfd.fasta " />
-    <param name="input" value="KP012_S64.scfd.fasta " />
-        <param name="r" value="-r"/>
-<param name="kaptive_k" value="--kaptive_k"/>
-<param name="kaptive_o" value=""/>
-        <output name="output" file="Kleborate_results.txt" />
-    </test>
-</tests>
-
-  <help>
-For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki)
-  </help>
-  <citations>
-    <citation type="doi">10.1101/2020.12.14.422303</citation>
-    <citation type="doi">10.1038/s41467-021-24448-3</citation>
-    <citation type="doi">10.1099/mgen.0.000102</citation>
-  </citations> 
-</tool>