# HG changeset patch
# User petr-novak
# Date 1690979319 0
# Node ID b50db133106a729bbfd4dc717b723e7f7f4df59c
# Parent  36c418bca8b27ad3037c244c885dcc8c5ad4f5c2
planemo upload commit 20bdf879b52796d3fb251a20807191ff02084d3c-dirty

diff -r 36c418bca8b2 -r b50db133106a extract_contigs_from_archive.xml
--- a/extract_contigs_from_archive.xml	Wed Aug 02 11:50:25 2023 +0000
+++ b/extract_contigs_from_archive.xml	Wed Aug 02 12:28:39 2023 +0000
@@ -1,10 +1,17 @@
-<tool id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive" version="1.0.0.3">
+<tooll id="extract_contigs" name="Extract contigs from RepeatExplorer2 archive" version="1.0.0.3">
   <command detect_errors="exit_code">
-    unzip -p ${RepeatExplorer_archive} contigs.fasta  &gt; ${contigs}
-    &amp;&amp;
-    unzip -p -j ${RepeatExplorer_archive} "*.aln"  &gt; ${aln}
+     <![CDATA[
+    unzip -p ${RepeatExplorer_archive} contigs.fasta  > ${contigs}
+    &&
+    unzip ${RepeatExplorer_archive} "*.aln" -d tempdir
+    &&
+    find tempdir -type f -name "*.aln" -exec cat {} + > ${aln}
+    &&
+    rm -r tempdir
+    ]]>
   </command>
 
+
   <inputs>
     <param name="RepeatExplorer_archive" label="Archive with RepeatExplorer2 results" type="data" format="zip"/>
   </inputs>
@@ -13,4 +20,4 @@
     <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>
+</tooll>