diff fastq_quality_boxplot.xml @ 4:439eed933bf9 draft

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

--- a/fastq_quality_boxplot.xml	Mon Jul 21 15:09:50 2014 -0400
+++ b/fastq_quality_boxplot.xml	Tue May 08 12:49:29 2018 -0400
@@ -1,19 +1,32 @@
-<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.0">
-	<description></description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-	<command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o $output</command>
-	
-	<inputs>
-		<param format="txt" name="input" type="data" label="Statistics report file"  help="output of 'FASTQ Statistics' tool" />
-	</inputs>
+<tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot" version="1.0.1">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+#set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($input.element_identifier))
+fastq_quality_boxplot_graph.sh
+-t '$escaped_element_identifier'
+-i '$input'
+-o '$output'
+    ]]></command>
 
-	<outputs>
-		<data format="png" name="output" metadata_source="input" />
-	</outputs>
-<help>
+    <inputs>
+        <param name="input" type="data" format="txt" label="Statistics report file"  help="output of 'FASTQ Statistics' tool" />
+    </inputs>
 
+    <outputs>
+        <data name="output" format="png" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="fastq_quality_boxplot-in1.fastq" />
+            <output name="output" file="fastq_quality_boxplot-out1.png" compare="sim_size" delta="768" />
+        </test>
+    </tests>
+    <help><![CDATA[
 **What it does**
 
 Creates a boxplot graph for the quality scores in the library.
@@ -49,9 +62,7 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-
-
-
-</help>
+    ]]></help>
+    <expand macro="citations" />
 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->
 </tool>