diff fastx_quality_statistics.xml @ 3:59003d0543cd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_quality_statistics commit bbb2e6b6769b03602a8ab97001f88fbec52080a1

--- a/fastx_quality_statistics.xml	Wed Nov 11 12:39:32 2015 -0500
+++ b/fastx_quality_statistics.xml	Tue May 08 13:28:00 2018 -0400
@@ -1,19 +1,20 @@
-<tool id="cshl_fastx_quality_statistics" version="1.0.0" name="Compute quality statistics">
+<tool id="cshl_fastx_quality_statistics" version="1.0.1" name="Compute quality statistics">
     <description></description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-zcat -f < '$input' | fastx_quality_stats -o '$output' -Q 33
-]]>
-    </command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_quality_stats
+-o '$output'
+@FQQUAL@
+    ]]></command>
 
     <inputs>
-        <param format="fastqsanger" name="input" type="data" label="Library to analyse" />
+        <expand macro="fastq_input" />
     </inputs>
     <outputs>
-        <data format="txt" name="output" metadata_source="input" />
+        <data name="output" format="txt" metadata_source="input" />
     </outputs>
     <tests>
         <test>
@@ -21,7 +22,7 @@
             <output name="output" file="fastq_stats1.out" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 Creates quality statistics report for the given Solexa/FASTQ library.
@@ -52,7 +53,6 @@
 * T_Count    = Count of 'T' nucleotides found in this column.
 * N_Count = Count of 'N' nucleotides found in this column.
 
-
 For example::
 
      1  6362991 -4 40 250734117 39.41 40 40 40  0 40 40 1396976 1329101  678730 2958184   0
@@ -66,6 +66,7 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
+    ]]></help>
+    <expand macro="citations" />
 <!-- FASTQ-Statistics is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->
 </tool>