Mercurial > repos > iuc > feelnc

annotate feelnc_wrapper.xml @ 4:fbe90d8cf66f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:08:19 +0000
parents caf522f98191
children 50718d48252c
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6284ec126e6a 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="0.2">
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3 <description>FlExible Extraction of LncRNA</description>
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4 <xrefs>
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5 <xref type="bio.tools">feelnc</xref>
fbe90d8cf66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 </xrefs>
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7 <requirements>
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8 <requirement type="package" version="0.2">feelnc</requirement>
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9 </requirements>
6284ec126e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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10 <command detect_errors="aggressive"><![CDATA[
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11 export FEELNCPATH=\$(dirname \$(command -v FEELnc_pipeline.sh))/../ &&
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12
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13 FEELnc_pipeline.sh
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14 --candidate='${candidate}'
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15 --reference='${reference}'
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16 --genome='${genome}'
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17 --outname='candidate_lncRNA'
6284ec126e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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18 --outdir='out_feelnc'
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20 &&
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22 cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log
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23 ]]></command>
6284ec126e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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24 <inputs>
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25 <param argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
caf522f98191 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
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26 <param argument="--reference" type="data" format="gtf" label="Reference annotation" />
caf522f98191 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
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27 <param argument="--genome" type="data" format="fasta" label="Genome sequence" />
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28 </inputs>
6284ec126e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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29 <outputs>
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30 <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}" />
6284ec126e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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31 <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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32 <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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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="candidate" value="transcript_chr38.gtf" />
caf522f98191 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
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37 <param name="reference" value="annotation_chr38.gtf" />
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38 <param name="genome" value="genome_chr38.fa" />
6284ec126e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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39 <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" />
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40 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" />
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41 <output name="classifier" file="candidate_lncRNA.classifier.txt" compare="sim_size" />
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 **What it does**
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46
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47 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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49 --------
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51 **Project links:**
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53 https://github.com/tderrien/FEELnc
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54 ]]></help>
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55 <citations>
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56 <citation type="doi">10.1093/nar/gkw1306</citation>
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57 </citations>
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58 </tool>