Mercurial > repos > petr-novak > re_utils

diff extract_contigs_from_archive.xml @ 2:ff658cf87f16 draft

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Uploaded
author petr-novak
date Wed, 04 Sep 2019 07:33:42 -0400
parents 2e811f988e1d
children c2c69c6090f0
line wrap: on
line diff
--- a/extract_contigs_from_archive.xml	Wed Jun 12 08:19:09 2019 -0400
+++ b/extract_contigs_from_archive.xml	Wed Sep 04 07:33:42 2019 -0400
@@ -1,6 +1,8 @@
 <tool id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive">
   <command detect_errors="exit_code">
     unzip -p ${RepeatExplorer_archive} contigs.fasta  &gt; ${contigs}
+    &amp;&amp;
+    unzip -p -j ${RepeatExplorer_archive} "*.aln"  &gt; ${aln}
   </command>
 
   <inputs>
@@ -8,6 +10,7 @@
   </inputs>
 
   <outputs>
-    <data name="contigs" format="fasta" label="contigs from RepeatExplorer clustering - data ${RepeatExplorer_archive.hid}" />
+    <data name="contigs" format="fasta" label="contigs from RepeatExplorer clustering from data ${RepeatExplorer_archive.hid}" />
+    <data name="aln" format="txt" label="contigs from RepeatExplorer clustering in aln format from data ${RepeatExplorer_archive.hid}" />
   </outputs>
 </tool>