# HG changeset patch
# User dazeone
# Date 1641916701 0
# Node ID aee729560f18b077483a2e37cdc987394debe60d
# Parent  67f31d0be358e67fa8d1cbdc5deb5c7306ce46c9
Uploaded

diff -r 67f31d0be358 -r aee729560f18 kleborate.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kleborate.xml	Tue Jan 11 15:58:21 2022 +0000
@@ -0,0 +1,70 @@
+<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>