Mercurial > repos > petr-novak > repeat_annotation_pipeline3

diff format_repeat_library.xml @ 11:5366d5ea04bc draft

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planemo upload commit 9d1b19f98d8b7f0a0d1baf2da63a373d155626f8-dirty
author petr-novak
date Fri, 04 Aug 2023 12:35:32 +0000
parents ea6a3059a6af
children
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--- a/format_repeat_library.xml	Thu May 04 09:27:43 2023 +0000
+++ b/format_repeat_library.xml	Fri Aug 04 12:35:32 2023 +0000
@@ -2,8 +2,11 @@
     <requirements>
         <requirement type="package" version="2.60.0">bioconductor-biostrings</requirement>
     </requirements>
+    <required_files>
+        <include type="literal" path="annotate_contigs.R"/>
+    </required_files>
     <command detect_errors="exit_code"><![CDATA[
-        $__tool_directory__/annotate_contigs.R '$contigs' '$cluster_table' '$annotated_contigs'
+        Rscript $__tool_directory__/annotate_contigs.R '$contigs' '$cluster_table' '$annotated_contigs'
     ]]></command>
     <inputs>
         <param type="data" name="contigs" format="fasta" label="Contigs - Library of Repeats from TAREAN/RepeatExplorer pipeline" />
@@ -60,7 +63,7 @@
 
 Clusters with higher number than those in CLUSTER_TABLE are removed from Repeat library
 
-Contigs are provided in followinf format::
+Contigs are provided in following format::
 
 
      >CL25Contig1