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comparison feelnc_wrapper.xml @ 0:b36afbb04e1c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
author iuc
date Wed, 28 Mar 2018 13:14:02 -0400
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1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1">
3 <description>FlExible Extraction of LncRNA</description>
4 <requirements>
5 <requirement type="package" version="0.1.1">feelnc</requirement>
6 </requirements>
7 <command detect_errors="aggressive"><![CDATA[
8 FEELnc_pipeline.sh
9 --candidate='${transcripts}'
10 --reference='${annotation}'
11 --genome='${genome}'
12 --outname='candidate_lncRNA'
13 --outdir='out_feelnc'
14 ]]></command>
15 <inputs>
16 <param name="transcripts" argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
17 <param name="annotation" argument="--reference" type="data" format="gtf" label="Reference annotation" />
18 <param name="genome" argument="--genome" type="data" format="fasta" label="Genome sequence" />
19 </inputs>
20 <outputs>
21 <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}" />
22 <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}" />
23 </outputs>
24 <tests>
25 <test>
26 <param name="transcripts" value="transcript_chr38.gtf" />
27 <param name="annotation" value="annotation_chr38.gtf" />
28 <param name="genome" value="genome_chr38.fa" />
29 <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" />
30 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" />
31 </test>
32 </tests>
33 <help><![CDATA[
34 **What it does**
35
36 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).
37
38 --------
39
40 **Project links:**
41
42 https://github.com/tderrien/FEELnc
43 ]]></help>
44 <citations>
45 <citation type="doi">10.1093/nar/gkw1306</citation>
46 </citations>
47 </tool>