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annotate 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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b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
iuc
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1 <?xml version="1.0" encoding="utf-8"?>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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2 <tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1">
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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3 <description>FlExible Extraction of LncRNA</description>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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4 <requirements>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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5 <requirement type="package" version="0.1.1">feelnc</requirement>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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6 </requirements>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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7 <command detect_errors="aggressive"><![CDATA[
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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8 FEELnc_pipeline.sh
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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9 --candidate='${transcripts}'
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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10 --reference='${annotation}'
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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11 --genome='${genome}'
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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12 --outname='candidate_lncRNA'
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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13 --outdir='out_feelnc'
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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14 ]]></command>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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15 <inputs>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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16 <param name="transcripts" argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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17 <param name="annotation" argument="--reference" type="data" format="gtf" label="Reference annotation" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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18 <param name="genome" argument="--genome" type="data" format="fasta" label="Genome sequence" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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19 </inputs>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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20 <outputs>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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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}" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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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}" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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23 </outputs>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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24 <tests>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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25 <test>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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26 <param name="transcripts" value="transcript_chr38.gtf" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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27 <param name="annotation" value="annotation_chr38.gtf" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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28 <param name="genome" value="genome_chr38.fa" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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29 <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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30 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" />
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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31 </test>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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32 </tests>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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33 <help><![CDATA[
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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34 **What it does**
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35
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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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).
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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37
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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38 --------
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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39
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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40 **Project links:**
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41
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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42 https://github.com/tderrien/FEELnc
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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43 ]]></help>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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44 <citations>
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45 <citation type="doi">10.1093/nar/gkw1306</citation>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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46 </citations>
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47 </tool>