Mercurial > repos > devteam > fastq_quality_boxplot

diff macros.xml @ 3:7cf5b1d072b5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_boxplot commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 13:29:05 -0500
parents 3987db70a4b0
children 867ab348287d
line wrap: on
line diff
--- a/macros.xml	Tue May 08 13:26:13 2018 -0400
+++ b/macros.xml	Thu Jan 30 13:29:05 2020 -0500
@@ -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 +18,15 @@
             #end if
         ]]>
     </token>
+    <token name="@GZIP@">
+        <![CDATA[
+            #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
+                | gzip -c
+            #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
+                | bzip2 -c
+            #end if
+        ]]>
+    </token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>