<?xml version="1.0" encoding="utf-8"?>
<tool id="feelnc" name="FEELnc" profile="17.01" version="0.2">
    <description>FlExible Extraction of LncRNA</description>
    <xrefs>
        <xref type="bio.tools">feelnc</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="0.2">feelnc</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
export FEELNCPATH=\$(dirname \$(command -v FEELnc_pipeline.sh))/../ &&
## Symlink the genome FASTA to the working directory to avoid writing .index to inputdir
ln -s '$genome' genome_fa &&
FEELnc_pipeline.sh
--candidate='${candidate}'
--reference='${reference}'
--genome=genome_fa
--outname='candidate_lncRNA'
--outdir='out_feelnc'

&&

cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log
    ]]></command>
    <inputs>
        <param argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
        <param argument="--reference" type="data" format="gtf" label="Reference annotation" />
        <param 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}" />
        <data format="txt" name="classifier" from_work_dir="out_feelnc/classifier/candidate_lncRNA.classifier.txt" label="Classifier output with ${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="candidate" value="transcript_chr38.gtf" />
            <param name="reference" 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" />
            <output name="classifier" file="candidate_lncRNA.classifier.txt" compare="sim_size" />
        </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>