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comparison feelnc_wrapper.xml @ 1:17a77824c8e4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e
author iuc
date Wed, 25 Apr 2018 15:55:19 -0400
parents b36afbb04e1c
children 75427ceb32d1
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0:b36afbb04e1c 1:17a77824c8e4
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"> 2 <tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1.1">
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="0.1.1">feelnc</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 FEELnc_pipeline.sh 8 FEELnc_pipeline.sh
9 --candidate='${transcripts}' 9 --candidate='${transcripts}'
10 --reference='${annotation}' 10 --reference='${annotation}'
11 --genome='${genome}' 11 --genome='${genome}'
12 --outname='candidate_lncRNA' 12 --outname='candidate_lncRNA'
13 --outdir='out_feelnc' 13 --outdir='out_feelnc'
14
15 &&
16
17 cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log
14 ]]></command> 18 ]]></command>
15 <inputs> 19 <inputs>
16 <param name="transcripts" argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" /> 20 <param name="transcripts" argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
17 <param name="annotation" argument="--reference" type="data" format="gtf" label="Reference annotation" /> 21 <param name="annotation" argument="--reference" type="data" format="gtf" label="Reference annotation" />
18 <param name="genome" argument="--genome" type="data" format="fasta" label="Genome sequence" /> 22 <param name="genome" argument="--genome" type="data" format="fasta" label="Genome sequence" />
19 </inputs> 23 </inputs>
20 <outputs> 24 <outputs>
21 <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}" /> 25 <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}" />
22 <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}" /> 26 <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}" />
27 <data format="txt" name="classifier" from_work_dir="out_feelnc/classifier/candidate_lncRNA.classifier.txt" label="Classifier output with ${tool.name} on ${on_string}" />
23 </outputs> 28 </outputs>
24 <tests> 29 <tests>
25 <test> 30 <test>
26 <param name="transcripts" value="transcript_chr38.gtf" /> 31 <param name="transcripts" value="transcript_chr38.gtf" />
27 <param name="annotation" value="annotation_chr38.gtf" /> 32 <param name="annotation" value="annotation_chr38.gtf" />
28 <param name="genome" value="genome_chr38.fa" /> 33 <param name="genome" value="genome_chr38.fa" />
29 <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" /> 34 <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" />
30 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" /> 35 <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" />
36 <output name="classifier" file="candidate_lncRNA.classifier.txt" compare="sim_size" />
31 </test> 37 </test>
32 </tests> 38 </tests>
33 <help><![CDATA[ 39 <help><![CDATA[
34 **What it does** 40 **What it does**
35 41
36 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). 42 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).
37 43
38 -------- 44 --------
39 45
40 **Project links:** 46 **Project links:**
41 47