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changeset 13:9337dd1fbc66 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastqc commit 8991687e2ec5f75d3841c613ea5d8ffda0389654
author iuc
date Mon, 05 Jun 2017 13:49:57 -0400
parents 484e86282f4b
children f2e8552cf1d0
files rgFastQC.xml
diffstat 1 files changed, 8 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/rgFastQC.xml	Mon May 15 08:34:57 2017 -0400
+++ b/rgFastQC.xml	Mon Jun 05 13:49:57 2017 -0400
@@ -1,22 +1,18 @@
-<tool id="fastqc" name="FastQC" version="0.68">
+<tool id="fastqc" name="FastQC" version="0.69">
     <description>Read Quality reports</description>
     <requirements>
         <requirement type="package" version="0.11.5">fastqc</requirement>
     </requirements>
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
-    <command><![CDATA[
-        python '${__tool_directory__}/rgFastQC.py'
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+        #set input_name = re.sub('[^\w\-\s]', '_', str($input_file.element_identifier))
+        python '$__tool_directory__/rgFastQC.py'
             -i '$input_file'
-            -d '${html_file.files_path}'
+            -d '$html_file.files_path'
             -o '$html_file'
             -t '$text_file'
-            -f '${input_file.ext}'
-            -j '${input_file.name}'
+            -f '$input_file.ext'
+            -j '$input_name'
             #if $contaminants.dataset and str($contaminants) > ''
                 -c '$contaminants'
             #end if