Mercurial > repos > devteam > fastq_quality_filter

changeset 5:b4c9c66a7a4d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastq_quality_filter commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 18:25:57 +0000
parents a55430a1c754
children c09c936532f0
files fastq_quality_filter.xml macros.xml
diffstat 2 files changed, 8 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/fastq_quality_filter.xml	Wed Aug 22 11:02:06 2018 -0400
+++ b/fastq_quality_filter.xml	Thu Jan 30 18:25:57 2020 +0000
@@ -1,17 +1,18 @@
-<tool id="cshl_fastq_quality_filter" version="1.0.2" name="Filter by quality">
+<tool id="cshl_fastq_quality_filter" version="1.0.2+galaxy0" name="Filter by quality">
     <description></description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="1.0.8">bzip2</requirement>
+    </expand>
     <command detect_errors="exit_code"><![CDATA[
 @CATS@ fastq_quality_filter
 -q $quality
 -p $percent
 -v
--o '$output'
 @FQQUAL@
-@GZIP@
+@GZIP@ > '$output'
     ]]></command>
 
     <inputs>
--- a/macros.xml	Wed Aug 22 11:02:06 2018 -0400
+++ b/macros.xml	Thu Jan 30 18:25:57 2020 +0000
@@ -21,7 +21,9 @@
     <token name="@GZIP@">
         <![CDATA[
             #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
-                -z
+                | gzip -c
+            #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
+                | bzip2 -c
             #end if
         ]]>
     </token>