# HG changeset patch
# User devteam
# Date 1444754383 14400
# Node ID 253c7f4976e3471f75543d693ec8897abb7da42e
# Parent  ee975578075f4aad2b8c7aca971edaabbeb82a1f
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

diff -r ee975578075f -r 253c7f4976e3 fastq_quality_converter.xml
--- a/fastq_quality_converter.xml	Tue Aug 20 10:37:12 2013 -0400
+++ b/fastq_quality_converter.xml	Tue Oct 13 12:39:43 2015 -0400
@@ -1,68 +1,68 @@
 <tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.0">
-	<description>(ASCII-Numeric)</description>
+    <description>(ASCII-Numeric)</description>
     <requirements>
         <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
     </requirements>
-	<command>zcat -f $input | fastq_quality_converter $QUAL_FORMAT -o $output -Q $offset</command>
-	<inputs>
-		<param format="fastq" name="input" type="data" label="Library to convert" />
+    <command>
+<![CDATA[
+zcat -f < '$input' | fastq_quality_converter $QUAL_FORMAT -o '$output' -Q $offset
+]]>
+    </command>
+    <inputs>
+        <param format="fastq" name="input" type="data" label="Library to convert" />
 
-		<param name="QUAL_FORMAT" type="select" label="Desired output format">
-			<option value="-a">ASCII (letters) quality scores</option>
-			<option value="-n">Numeric quality scores</option>
-		</param>
-		
+        <param name="QUAL_FORMAT" type="select" label="Desired output format">
+            <option value="-a">ASCII (letters) quality scores</option>
+            <option value="-n">Numeric quality scores</option>
+        </param>
+
         <param name="offset" type="select" label="FASTQ ASCII offset">
             <option value="33">33</option>
             <option selected="true" value="64">64</option>
-        </param>	
+        </param>
     </inputs>
-
-	<tests>
-		<test>
-			<!-- ASCII to NUMERIC -->
-			<param name="input" value="fastq_qual_conv1.fastq" />
-			<param name="QUAL_FORMAT" value="Numeric quality scores" />
-			<param name="offset" value="64" />
-			<output name="output" file="fastq_qual_conv1.out" />
-		</test>
-		<test>
-			<!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output -->
-			<param name="input" value="fastq_qual_conv1.fastq" />
-			<param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
-			<param name="offset" value="64" />
-			<output name="output" file="fastq_qual_conv1a.out" />
-		</test>
-		<test>
-			<!-- NUMERIC to ASCII -->
-			<param name="input" value="fastq_qual_conv2.fastq" />
-			<param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
-			<param name="offset" value="64" />
-			<output name="output" file="fastq_qual_conv2.out" />
-		</test>
-		<test>
-			<!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output -->
-			<param name="input" value="fastq_qual_conv2.fastq" />
-			<param name="QUAL_FORMAT" value="Numeric quality scores" />
-			<param name="offset" value="64" />
-			<output name="output" file="fastq_qual_conv2n.out" />
-		</test>
-	</tests>
-
-	<outputs>
-		<data format="fastq" name="output" metadata_source="input" />
-	</outputs>
-<help>
-
+    <outputs>
+        <data format="fastq" name="output" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- ASCII to NUMERIC -->
+            <param name="input" value="fastq_qual_conv1.fastq" />
+            <param name="QUAL_FORMAT" value="Numeric quality scores" />
+            <param name="offset" value="64" />
+            <output name="output" file="fastq_qual_conv1.out" />
+        </test>
+        <test>
+            <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output -->
+            <param name="input" value="fastq_qual_conv1.fastq" />
+            <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
+            <param name="offset" value="64" />
+            <output name="output" file="fastq_qual_conv1a.out" />
+        </test>
+        <test>
+            <!-- NUMERIC to ASCII -->
+            <param name="input" value="fastq_qual_conv2.fastq" />
+            <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
+            <param name="offset" value="64" />
+            <output name="output" file="fastq_qual_conv2.out" />
+        </test>
+        <test>
+            <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output -->
+            <param name="input" value="fastq_qual_conv2.fastq" />
+            <param name="QUAL_FORMAT" value="Numeric quality scores" />
+            <param name="offset" value="64" />
+            <output name="output" file="fastq_qual_conv2n.out" />
+        </test>
+    </tests>
+    <help>
 **What it does**
 
 Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
 
-.. class:: warningmark 
+.. class:: warningmark
 
 Re-scaling is **not** performed. (e.g. conversion from Phred scale to Solexa scale).
 
-
 -----
 
 FASTQ with Numeric quality scores::
@@ -93,7 +93,6 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
- 
-</help>
+    </help>
 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
 </tool>
diff -r ee975578075f -r 253c7f4976e3 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Aug 20 10:37:12 2013 -0400
+++ b/tool_dependencies.xml	Tue Oct 13 12:39:43 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="fastx_toolkit" version="0.0.13">
-        <repository changeset_revision="1cd326991d32" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="e76e81b3eccf" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>