diff feelnc_wrapper.xml @ 1:17a77824c8e4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/feelnc commit 1b1520d42f96f78662e75bce1e899a57b052ec1e

--- a/feelnc_wrapper.xml	Wed Mar 28 13:14:02 2018 -0400
+++ b/feelnc_wrapper.xml	Wed Apr 25 15:55:19 2018 -0400
@@ -1,16 +1,20 @@
 <?xml version="1.0" encoding="utf-8"?>
-<tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1">
+<tool id="feelnc" name="FEELnc" profile="17.01" version="0.1.1.1">
     <description>FlExible Extraction of LncRNA</description>
     <requirements>
         <requirement type="package" version="0.1.1">feelnc</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
-FEELnc_pipeline.sh 
+FEELnc_pipeline.sh
 --candidate='${transcripts}'
 --reference='${annotation}'
---genome='${genome}' 
+--genome='${genome}'
 --outname='candidate_lncRNA'
 --outdir='out_feelnc'
+
+&&
+
+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" />
@@ -20,6 +24,7 @@
     <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}" />
         <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}" />
+        <data format="txt" name="classifier" from_work_dir="out_feelnc/classifier/candidate_lncRNA.classifier.txt" label="Classifier output with ${tool.name} on ${on_string}" />
     </outputs>
     <tests>
         <test>
@@ -28,12 +33,13 @@
             <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" />
+            <output name="classifier" file="candidate_lncRNA.classifier.txt" compare="sim_size" />
         </test>
     </tests>
     <help><![CDATA[
 **What it does**
 
-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). 
+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).
 
 --------