--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/feelnc_wrapper.xml	Wed Mar 28 13:14:02 2018 -0400
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1">
+    <description>FlExible Extraction of LncRNA</description>
+    <requirements>
+        <requirement type="package" version="0.1.1">feelnc</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+FEELnc_pipeline.sh 
+--candidate='${transcripts}'
+--reference='${annotation}'
+--genome='${genome}' 
+--outname='candidate_lncRNA'
+--outdir='out_feelnc'
+    ]]></command>
+    <inputs>
+        <param name="transcripts" argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
+        <param name="annotation" argument="--reference" type="data" format="gtf" label="Reference annotation" />
+        <param name="genome" argument="--genome" type="data" format="fasta" label="Genome sequence" />
+    </inputs>
+    <outputs>
+        <data format="gtf" name="candidate_lncRNA" from_work_dir="out_feelnc/codpot/candidate_lncRNA.codpot.lncRNA.gtf" label="lncRNA annotation with ${tool.name} on ${on_string}" />
+        <data format="gtf" name="candidate_mRNA" from_work_dir="out_feelnc/codpot/candidate_lncRNA.codpot.mRNA.gtf" label="mRNA annotation with ${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="transcripts" value="transcript_chr38.gtf" />
+            <param name="annotation" value="annotation_chr38.gtf" />
+            <param name="genome" value="genome_chr38.fa" />
+            <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" />
+            <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+FEELnc pipeline is used to annotate long non-coding RNAs (lncRNAs) based on reconstructed transcripts from RNA-seq data (either with or without a reference genome). 
+
+--------
+
+**Project links:**
+
+https://github.com/tderrien/FEELnc
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkw1306</citation>
+    </citations>
+</tool>