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annotate feelnc_wrapper.xml @ 2:75427ceb32d1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit c39323361ef6ba2664646e4476736c80bcd01124"
author iuc
date Wed, 18 Dec 2019 15:24:23 -0500
parents 17a77824c8e4
children 095162ba8e90
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b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1.1">
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3 <description>FlExible Extraction of LncRNA</description>
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4 <requirements>
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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[
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75427ceb32d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit c39323361ef6ba2664646e4476736c80bcd01124"
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8 export FEELNCPATH=\$(dirname \$(command -v FEELnc_pipeline.sh))/../ &&
75427ceb32d1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit c39323361ef6ba2664646e4476736c80bcd01124"
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9
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10 FEELnc_pipeline.sh
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11 --candidate='${transcripts}'
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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12 --reference='${annotation}'
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13 --genome='${genome}'
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b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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14 --outname='candidate_lncRNA'
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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15 --outdir='out_feelnc'
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17 &&
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19 cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log
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20 ]]></command>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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21 <inputs>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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22 <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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23 <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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24 <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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25 </inputs>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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26 <outputs>
b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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27 <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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28 <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}" />
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29 <data format="txt" name="classifier" from_work_dir="out_feelnc/classifier/candidate_lncRNA.classifier.txt" label="Classifier output with ${tool.name} on ${on_string}" />
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b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="transcripts" value="transcript_chr38.gtf" />
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34 <param name="annotation" value="annotation_chr38.gtf" />
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35 <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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36 <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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37 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" />
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38 <output name="classifier" file="candidate_lncRNA.classifier.txt" compare="sim_size" />
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b36afbb04e1c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 **What it does**
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43
1
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44 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).
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45
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46 --------
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47
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48 **Project links:**
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49
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50 https://github.com/tderrien/FEELnc
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51 ]]></help>
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52 <citations>
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53 <citation type="doi">10.1093/nar/gkw1306</citation>
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54 </citations>
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55 </tool>