Mercurial > repos > devteam > fastx_barcode_splitter

diff macros.xml @ 5:da00153634dc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit b2735803f9719ff955a49a5bde54a211d6d48bb5
author iuc
date Thu, 11 Oct 2018 09:35:34 -0400
parents e3d91cb9f196
children 8da8564e2e45
line wrap: on
line diff
--- a/macros.xml	Tue May 08 12:50:59 2018 -0400
+++ b/macros.xml	Thu Oct 11 09:35:34 2018 -0400
@@ -2,7 +2,7 @@
 <macros>
     <token name="@CATS@">
         #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
-            zcat -f '$input' |
+            gunzip -c -f '$input' |
         #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
             bzcat -f '$input' |
         #else:
@@ -18,6 +18,13 @@
             #end if
         ]]>
     </token>
+    <token name="@GZIP@">
+        <![CDATA[
+            #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
+                -z
+            #end if
+        ]]>
+    </token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>