# HG changeset patch
# User devteam
# Date 1444754492 14400
# Node ID 76cefe061c3d3ef5e8e077e35e0da5cb14aedbb5
# Parent  8c60fa8ae153c8bbf45d8941ab7394c2ac912594
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

diff -r 8c60fa8ae153 -r 76cefe061c3d fastx_quality_statistics.xml
--- a/fastx_quality_statistics.xml	Tue Nov 26 12:49:06 2013 -0500
+++ b/fastx_quality_statistics.xml	Tue Oct 13 12:41:32 2015 -0400
@@ -1,27 +1,27 @@
 <tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics">
-	<description></description>
+    <description></description>
     <requirements>
         <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
     </requirements>
-	<command>zcat -f $input | fastx_quality_stats -o $output -Q 33</command>
-
-	<inputs>
-		<param format="fastqsanger" name="input" type="data" label="Library to analyse" />
-	</inputs>
+    <command>
+<![CDATA[
+zcat -f < '$input' | fastx_quality_stats -o '$output' -Q 33
+]]>
+    </command>
 
-	<tests>
-		<test>
-			<param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
-			<output name="output" file="fastq_stats1.out" />
-		</test>
-	</tests>
-
-	<outputs>
-		<data format="txt" name="output" metadata_source="input" />
-	</outputs>
-
-<help>
-
+    <inputs>
+        <param format="fastqsanger" name="input" type="data" label="Library to analyse" />
+    </inputs>
+    <outputs>
+        <data format="txt" name="output" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fastq_stats1.fastq" ftype="fastqsanger"/>
+            <output name="output" file="fastq_stats1.out" />
+        </test>
+    </tests>
+    <help>
 **What it does**
 
 Creates quality statistics report for the given Solexa/FASTQ library.
@@ -34,23 +34,23 @@
 
 **The output file will contain the following fields:**
 
-* column	= column number (1 to 36 for a 36-cycles read Solexa file)
+* column    = column number (1 to 36 for a 36-cycles read Solexa file)
 * count   = number of bases found in this column.
 * min     = Lowest quality score value found in this column.
 * max     = Highest quality score value found in this column.
 * sum     = Sum of quality score values for this column.
 * mean    = Mean quality score value for this column.
-* Q1	= 1st quartile quality score.
-* med	= Median quality score.
-* Q3	= 3rd quartile quality score.
-* IQR	= Inter-Quartile range (Q3-Q1).
-* lW	= 'Left-Whisker' value (for boxplotting).
-* rW	= 'Right-Whisker' value (for boxplotting).
-* A_Count	= Count of 'A' nucleotides found in this column.
-* C_Count	= Count of 'C' nucleotides found in this column.
-* G_Count	= Count of 'G' nucleotides found in this column.
-* T_Count	= Count of 'T' nucleotides found in this column.
-* N_Count = Count of 'N' nucleotides found in this column.  
+* Q1    = 1st quartile quality score.
+* med    = Median quality score.
+* Q3    = 3rd quartile quality score.
+* IQR    = Inter-Quartile range (Q3-Q1).
+* lW    = 'Left-Whisker' value (for boxplotting).
+* rW    = 'Right-Whisker' value (for boxplotting).
+* A_Count    = Count of 'A' nucleotides found in this column.
+* C_Count    = Count of 'C' nucleotides found in this column.
+* G_Count    = Count of 'G' nucleotides found in this column.
+* T_Count    = Count of 'T' nucleotides found in this column.
+* N_Count = Count of 'N' nucleotides found in this column.
 
 
 For example::
@@ -60,13 +60,12 @@
      3  6362991 -5 40 248722469 39.09 40 40 40  0 40 40 2296384  984875 1443989 1637743   0
      4  6362991 -4 40 248214827 39.01 40 40 40  0 40 40 2536861 1167423 1248968 1409739   0
     36  6362991 -5 40 117158566 18.41  7 15 30 23 -5 40 4074444 1402980   63287  822035 245
-    
+
 ------
 
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-
-</help>
+    </help>
 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
 </tool>
diff -r 8c60fa8ae153 -r 76cefe061c3d tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Nov 26 12:49:06 2013 -0500
+++ b/tool_dependencies.xml	Tue Oct 13 12:41:32 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>