Mercurial > repos > devteam > fasta_nucleotide_changer

changeset 4:091ca73f5804 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_nucleotide_changer commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
author iuc
date Wed, 22 Aug 2018 11:04:20 -0400
parents cc9a18dd41c9
children ec0b5076173a
files fasta_nucleotide_changer.xml macros.xml
diffstat 2 files changed, 10 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/fasta_nucleotide_changer.xml	Tue May 08 13:26:01 2018 -0400
+++ b/fasta_nucleotide_changer.xml	Wed Aug 22 11:04:20 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="cshl_fasta_nucleotides_changer" version="1.0.1" name="RNA/DNA" >
+<tool id="cshl_fasta_nucleotides_changer" version="1.0.2" name="RNA/DNA" >
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
@@ -9,6 +9,7 @@
 -$mode
 -v
 -o '$output'
+@GZIP@
     ]]></command>
     <inputs>
         <expand macro="fasta_input" />
--- a/macros.xml	Tue May 08 13:26:01 2018 -0400
+++ b/macros.xml	Wed Aug 22 11:04:20 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>