--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kat_sect.xml	Mon Feb 06 12:36:09 2017 -0500
@@ -0,0 +1,66 @@
+<tool id="kat_sect" name="KAT Sect" version="1.3.0">
+  <description> SEquence Coverage estimator Tool. Estimates the coverage of each sequence in a file using K-mers from another sequence file.</description>
+  <requirements>
+    <requirement type="package" version="2.3.1">kat</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+
+  ln "$db" db.fasta &&
+  #if $single_or_paired.type == "single"
+    ln "$input_se" "$single_or_paired.input_se.element_identifier".fastq && 
+    kat sect 'db.fasta'
+    "$single_or_paired.input_se.element_identifier".fastq
+  #elif $single_or_paired.type == "paired"
+    ln "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq &&
+    kat sect 'db.fasta'
+    "$single_or_paired.forward_pe.name"_1.fastq "$single_or_paired.forward_pe.name"_2.fastq
+  #else
+    ln "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq &&
+    kat sect 'db.fasta'
+    "$single_or_paired.fastq_collection.forward.name"_1.fastq "$single_or_paired.fastq_collection.forward.name"_2.fastq
+  #end if  
+  --threads \${GALAXY_SLOTS:-4}
+  -o reads
+  
+  ]]></command>
+  <inputs>
+    <conditional name="single_or_paired">
+      <param name="type" type="select" label="Read type">
+        <option value="single">Single-end</option>
+        <option value="paired">Paired-end</option>
+        <option value="collection">Collection Paired-end</option>
+      </param>
+      <when value="single">
+        <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
+      </when>
+      <when value="paired">
+        <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
+        <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
+      </when>
+      <when value="collection">
+        <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
+      </when>
+    </conditional>
+    <param name="db" type="data" format="fasta" label="Fasta file of targeted regions"/>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="reads" label='Reads' from_work_dir="reads-stats.tsv" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="input.fastq" />
+      <param name="db" value="db.fasta" />
+      <output file="matched.fastq" ftype="fastqsanger" name="reads" />
+    </test>
+  </tests>
+  <help><![CDATA[
+http://kat.readthedocs.io/en/latest/using.html#filtering-tools
+]]>
+  
+  </help>
+  <citations>
+  </citations>
+</tool>