diff fasta_formatter.xml @ 2:9457a20156db draft

planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

--- a/fasta_formatter.xml	Tue Dec 03 12:36:12 2013 -0500
+++ b/fasta_formatter.xml	Mon Oct 12 10:15:31 2015 -0400
@@ -1,48 +1,49 @@
 <tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width">
-	<description>formatter</description>
+    <description>formatter</description>
     <requirements>
         <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
     </requirements>
-	<!--
-		Note:
-			fasta_formatter also has a tabular output mode (-t),
-			but Galaxy already contains such a tool, so no need
-			to offer the user a duplicated tool.
+    <!--
+        Note:
+            fasta_formatter also has a tabular output mode (-t),
+            but Galaxy already contains such a tool, so no need
+            to offer the user a duplicated tool.
 
-			So this XML tool only changes the width (line-wrapping) of a
-			FASTA file.
-	-->
-	<command>zcat -f '$input' | fasta_formatter -w $width -o $output</command>
-	<inputs>
-		<param format="fasta" name="input" type="data" label="Library to re-format" />
-
-		<param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
-	</inputs>
+            So this XML tool only changes the width (line-wrapping) of a
+            FASTA file.
+    -->
+    <command>
+<![CDATA[
+zcat -f < '$input' | fasta_formatter -w $width -o '$output'
+]]>
+    </command>
+    <inputs>
+        <param format="fasta" name="input" type="data" label="Library to re-format" />
 
-	<tests>
-		<test>
-			<!-- Re-format a FASTA file into a single line -->
-			<param name="input" value="fasta_formatter1.fasta" /> 
-			<param name="width" value="0" />
-			<param name="output" file="fasta_formatter1.out" />
-		</test>
-		<test>
-			<!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
-			<param name="input" value="fasta_formatter1.fasta" />
-			<param name="width" value="60" />
-			<param name="output" file="fasta_formatter2.out" />
-		</test>
-	</tests>
-
-	<outputs>
-		<data format="input" name="output" metadata_source="input" />
-	</outputs>
-
-<help>
+        <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" metadata_source="input" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- Re-format a FASTA file into a single line -->
+            <param name="input" value="fasta_formatter1.fasta" />
+            <param name="width" value="0" />
+            <output name="output" file="fasta_formatter1.out" />
+        </test>
+        <test>
+            <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
+            <param name="input" value="fasta_formatter1.fasta" />
+            <param name="width" value="60" />
+            <output name="output" file="fasta_formatter2.out" />
+        </test>
+    </tests>
+    <help>
 **What it does**
 
 This tool re-formats a FASTA file, changing the width of the nucleotides lines.
-  
+
 **TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line.
 
 --------
@@ -84,6 +85,5 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
- 
-</help>
+    </help>
 </tool>