# HG changeset patch
# User iuc
# Date 1691650307 0
# Node ID 1e76bd67fb734fb012b5c25eb12f2d6881eaf5c7
# Parent  7bda0f25191f2ab1277b85b8e8f2abdd23c9362f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_collapser commit fd099d17eceaa319fbfe429f4725328d88b18c9f

diff -r 7bda0f25191f -r 1e76bd67fb73 fastx_collapser.xml
--- a/fastx_collapser.xml	Tue May 08 12:51:34 2018 -0400
+++ b/fastx_collapser.xml	Thu Aug 10 06:51:47 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="cshl_fastx_collapser" version="1.0.1" name="Collapse">
+<tool id="cshl_fastx_collapser" version="1.0.1+galaxy@VERSION_SUFFIX@" profile="22.05" name="Collapse">
     <description>sequences</description>
     <macros>
         <import>macros.xml</import>
diff -r 7bda0f25191f -r 1e76bd67fb73 macros.xml
--- a/macros.xml	Tue May 08 12:51:34 2018 -0400
+++ b/macros.xml	Thu Aug 10 06:51:47 2023 +0000
@@ -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>
@@ -25,6 +34,7 @@
         </requirements>
     </xml>
     <token name="@VERSION@">0.0.14</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@SANGER@">fastqsanger,fastqsanger.gz,fastqsanger.bz2</token>
     <token name="@SOLEXA@">fastqsolexa,fastqsolexa.gz,fastqsolexa.bz2</token>
     <token name="@ILLUMINA@">fastqillumina,fastqillumina.gz,fastqillumina.bz2</token>