Mercurial > repos > iuc > feelnc

comparison feelnc_wrapper.xml @ 3:095162ba8e90 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 68cd9a8ae50c5dfe6b667062a5172010511bcaff"
author iuc
date Tue, 01 Dec 2020 10:55:23 +0000
parents 75427ceb32d1
children 67af24676bd6
comparison
equal deleted inserted replaced
2:75427ceb32d1 3:095162ba8e90
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1.1"> 2 <tool id="feelnc" name="FEELnc" profile="17.01" version="0.2">
3 <description>FlExible Extraction of LncRNA</description> 3 <description>FlExible Extraction of LncRNA</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="0.1.1">feelnc</requirement> 5 <requirement type="package" version="0.2">feelnc</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 export FEELNCPATH=\$(dirname \$(command -v FEELnc_pipeline.sh))/../ && 8 export FEELNCPATH=\$(dirname \$(command -v FEELnc_pipeline.sh))/../ &&
9 9
10 FEELnc_pipeline.sh 10 FEELnc_pipeline.sh
11 --candidate='${transcripts}' 11 --candidate='${candidate}'
12 --reference='${annotation}' 12 --reference='${reference}'
13 --genome='${genome}' 13 --genome='${genome}'
14 --outname='candidate_lncRNA' 14 --outname='candidate_lncRNA'
15 --outdir='out_feelnc' 15 --outdir='out_feelnc'
16 16
17 && 17 &&
18 18
19 cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log 19 cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log
20 ]]></command> 20 ]]></command>
21 <inputs> 21 <inputs>
22 <param name="transcripts" argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" /> 22 <param argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
23 <param name="annotation" argument="--reference" type="data" format="gtf" label="Reference annotation" /> 23 <param argument="--reference" type="data" format="gtf" label="Reference annotation" />
24 <param name="genome" argument="--genome" type="data" format="fasta" label="Genome sequence" /> 24 <param argument="--genome" type="data" format="fasta" label="Genome sequence" />
25 </inputs> 25 </inputs>
26 <outputs> 26 <outputs>
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}" /> 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}" />
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}" /> 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}" />
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}" /> 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}" />
30 </outputs> 30 </outputs>
31 <tests> 31 <tests>
32 <test> 32 <test>
33 <param name="transcripts" value="transcript_chr38.gtf" /> 33 <param name="candidate" value="transcript_chr38.gtf" />
34 <param name="annotation" value="annotation_chr38.gtf" /> 34 <param name="reference" value="annotation_chr38.gtf" />
35 <param name="genome" value="genome_chr38.fa" /> 35 <param name="genome" value="genome_chr38.fa" />
36 <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" /> 36 <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" />
37 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" /> 37 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" />
38 <output name="classifier" file="candidate_lncRNA.classifier.txt" compare="sim_size" /> 38 <output name="classifier" file="candidate_lncRNA.classifier.txt" compare="sim_size" />
39 </test> 39 </test>