Mercurial > repos > iuc > feelnc
annotate feelnc_wrapper.xml @ 4:67af24676bd6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8913264abbcee238b5ef81268d111db98c942bfe"
author | iuc |
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date | Thu, 23 Sep 2021 18:18:45 +0000 |
parents | 095162ba8e90 |
children | 55daa4712413 |
rev | line source |
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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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095162ba8e90
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
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2 <tool id="feelnc" name="FEELnc" profile="17.01" version="0.2"> |
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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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3 <description>FlExible Extraction of LncRNA</description> |
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67af24676bd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8913264abbcee238b5ef81268d111db98c942bfe"
iuc
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4 <xrefs> |
67af24676bd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8913264abbcee238b5ef81268d111db98c942bfe"
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5 <xref type="bio.tools">feelnc</xref> |
67af24676bd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8913264abbcee238b5ef81268d111db98c942bfe"
iuc
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6 </xrefs> |
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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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7 <requirements> |
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095162ba8e90
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
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8 <requirement type="package" version="0.2">feelnc</requirement> |
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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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9 </requirements> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
iuc
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10 <command detect_errors="aggressive"><![CDATA[ |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit c39323361ef6ba2664646e4476736c80bcd01124"
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11 export FEELNCPATH=\$(dirname \$(command -v FEELnc_pipeline.sh))/../ && |
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67af24676bd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8913264abbcee238b5ef81268d111db98c942bfe"
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12 ## Symlink the genome FASTA to the working directory to avoid writing .index to inputdir |
67af24676bd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8913264abbcee238b5ef81268d111db98c942bfe"
iuc
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13 ln -s '$genome' genome_fa && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e
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14 FEELnc_pipeline.sh |
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095162ba8e90
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
iuc
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15 --candidate='${candidate}' |
095162ba8e90
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
iuc
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16 --reference='${reference}' |
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67af24676bd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 8913264abbcee238b5ef81268d111db98c942bfe"
iuc
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17 --genome=genome_fa |
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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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18 --outname='candidate_lncRNA' |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
iuc
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19 --outdir='out_feelnc' |
1
17a77824c8e4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e
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20 |
17a77824c8e4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e
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21 && |
17a77824c8e4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e
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22 |
17a77824c8e4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e
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23 cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
iuc
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24 ]]></command> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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25 <inputs> |
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095162ba8e90
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
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26 <param argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" /> |
095162ba8e90
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
iuc
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27 <param argument="--reference" type="data" format="gtf" label="Reference annotation" /> |
095162ba8e90
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
iuc
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28 <param argument="--genome" type="data" format="fasta" label="Genome sequence" /> |
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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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29 </inputs> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
iuc
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30 <outputs> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
iuc
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31 <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
iuc
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32 <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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17a77824c8e4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e
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33 <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
iuc
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34 </outputs> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
iuc
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35 <tests> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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36 <test> |
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095162ba8e90
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
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37 <param name="candidate" value="transcript_chr38.gtf" /> |
095162ba8e90
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
iuc
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38 <param name="reference" value="annotation_chr38.gtf" /> |
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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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39 <param name="genome" value="genome_chr38.fa" /> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
iuc
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40 <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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41 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e
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42 <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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43 </test> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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44 </tests> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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45 <help><![CDATA[ |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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46 **What it does** |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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47 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e
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48 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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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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49 |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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50 -------- |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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51 |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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52 **Project links:** |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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53 |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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54 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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55 ]]></help> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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56 <citations> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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57 <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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58 </citations> |
b36afbb04e1c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit e56ef992726eb29b7a24842fde2c052a92214016
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59 </tool> |