Mercurial > repos > iuc > feelnc

diff feelnc_wrapper.xml @ 3:095162ba8e90 draft

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"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
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--- a/feelnc_wrapper.xml	Wed Dec 18 15:24:23 2019 -0500
+++ b/feelnc_wrapper.xml	Tue Dec 01 10:55:23 2020 +0000
@@ -1,15 +1,15 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1.1">
+<tool id="feelnc" name="FEELnc" profile="17.01" version="0.2">
     <description>FlExible Extraction of LncRNA</description>
     <requirements>
-        <requirement type="package" version="0.1.1">feelnc</requirement>
+        <requirement type="package" version="0.2">feelnc</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 export FEELNCPATH=\$(dirname \$(command -v FEELnc_pipeline.sh))/../ &&
 
 FEELnc_pipeline.sh
---candidate='${transcripts}'
---reference='${annotation}'
+--candidate='${candidate}'
+--reference='${reference}'
 --genome='${genome}'
 --outname='candidate_lncRNA'
 --outdir='out_feelnc'
@@ -19,9 +19,9 @@
 cat out_feelnc/codpot/candidate_lncRNA.codpot_RF_summary.txt out_feelnc/classifier/candidate_lncRNA.classifier.log
     ]]></command>
     <inputs>
-        <param name="transcripts" argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
-        <param name="annotation" argument="--reference" type="data" format="gtf" label="Reference annotation" />
-        <param name="genome" argument="--genome" type="data" format="fasta" label="Genome sequence" />
+        <param argument="--candidate" type="data" format="gtf" label="Transcripts assembly" help="Stringtie or Cufflinks output" />
+        <param argument="--reference" type="data" format="gtf" label="Reference annotation" />
+        <param argument="--genome" type="data" format="fasta" label="Genome sequence" />
     </inputs>
     <outputs>
         <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}" />
@@ -30,8 +30,8 @@
     </outputs>
     <tests>
         <test>
-            <param name="transcripts" value="transcript_chr38.gtf" />
-            <param name="annotation" value="annotation_chr38.gtf" />
+            <param name="candidate" value="transcript_chr38.gtf" />
+            <param name="reference" value="annotation_chr38.gtf" />
             <param name="genome" value="genome_chr38.fa" />
             <output name="candidate_lncRNA" file="candidate_lncRNA.gtf.lncRNA-sort.gtf" sort="True" />
             <output name="candidate_mRNA" file="candidate_lncRNA.gtf.mRNA-sort.gtf" sort="True" />