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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8069a247dc205300cad852d383d610255af99dfa
author iuc
date Wed, 07 Dec 2022 19:34:37 +0000
parents 50718d48252c
children
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3063b598f93f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8069a247dc205300cad852d383d610255af99dfa
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1 <tool id="feelnc" name="FEELnc" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>FlExible Extraction of LncRNA</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.2.1</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">feelnc</xref>
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9 </xrefs>
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10 <requirements>
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11 <requirement type="package" version="0.2">feelnc</requirement>
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12 </requirements>
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13 <command detect_errors="aggressive"><![CDATA[
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14 export FEELNCPATH=\$(dirname \$(command -v FEELnc_pipeline.sh))/../ &&
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15 ## Symlink the genome FASTA to the working directory to avoid writing .index to inputdir
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16 ln -s '$genome' genome_fa &&
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17 FEELnc_pipeline.sh
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18 --candidate='${candidate}'
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19 --reference='${reference}'
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20 --genome=genome_fa
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21 --outname='candidate_lncRNA'
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22 --outdir='out_feelnc'
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24 &&
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26 cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log
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27 ]]></command>
6284ec126e6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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28 <inputs>
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29 <param argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
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30 <param argument="--reference" type="data" format="gtf" label="Reference annotation" />
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31 <param argument="--genome" type="data" format="fasta" label="Genome sequence" />
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32 </inputs>
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33 <outputs>
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34 <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}" />
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35 <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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36 <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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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="candidate" value="transcript_chr38.gtf" />
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41 <param name="reference" value="annotation_chr38.gtf" />
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42 <param name="genome" value="genome_chr38.fa" />
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43 <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" />
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44 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" />
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45 <output name="classifier" file="candidate_lncRNA.classifier.txt" compare="sim_size" />
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 **What it does**
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50
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51 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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53 --------
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55 **Project links:**
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57 https://github.com/tderrien/FEELnc
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58 ]]></help>
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59 <citations>
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60 <citation type="doi">10.1093/nar/gkw1306</citation>
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61 </citations>
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62 </tool>