Mercurial > repos > galaxy-australia > hifiadapterfilt

diff macros.xml @ 0:bbc2060caa0e draft

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"
author galaxy-australia
date Mon, 11 Jul 2022 03:09:58 +0000
parents
children 03acc0e3772e
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Jul 11 03:09:58 2022 +0000
@@ -0,0 +1,29 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.0.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.05</token>
+    <token name="@DIGEST@">99b5e479baee5ffe01c676dd3d7180b0d3eb94af08db0f2ceb3641bef3ebbaa4</token>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">dmolik/pbadapterfilt:latest</container>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+      <stdio>
+         <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+         <exit_code range="1:"  level="fatal" description="Error" />
+      </stdio>
+    </xml>	
+    <token name="@CLEAN_EXT@">
+        <![CDATA[
+        #from os.path import splitext
+        #import re
+        #def clean_ext($identifier)
+            #while $identifier.endswith(('.fq','.fastq', '.fastq.gz','.bam'))
+                #set $identifier = splitext($identifier)[0]
+            #end while
+$identifier#slurp
+        #end def
+        ]]>
+    </token>
+</macros>