Mercurial > repos > devteam > fastx_clipper

changeset 5:b8658f852bc7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_clipper commit 4c002e52261da2e7609735883d91fa1610ce6ce7"
author iuc
date Thu, 30 Jan 2020 13:30:10 -0500
parents 736b8f6ee456
children cb1e251cac37
files fastx_clipper.xml macros.xml
diffstat 2 files changed, 8 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/fastx_clipper.xml	Wed Aug 22 11:05:15 2018 -0400
+++ b/fastx_clipper.xml	Thu Jan 30 13:30:10 2020 -0500
@@ -1,20 +1,21 @@
-<tool id="cshl_fastx_clipper" name="Clip" version="1.0.3">
+<tool id="cshl_fastx_clipper" name="Clip" version="1.0.3+galaxy0">
     <description>adapter sequences</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@ fastx_clipper
 -l $minlength
 -a '$clip_source.clip_sequence'
 -d $keepdelta
--o '$output'
 -v
 $KEEP_N
 $DISCARD_OPTIONS
 @FQQUAL@
-@GZIP@
+@GZIP@ > '$output'
     ]]></command>
 
     <inputs>
--- a/macros.xml	Wed Aug 22 11:05:15 2018 -0400
+++ b/macros.xml	Thu Jan 30 13:30:10 2020 -0500
@@ -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>