diff fasta_formatter.xml @ 3:859422bcb689 draft

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

--- a/fasta_formatter.xml	Mon Oct 12 10:15:31 2015 -0400
+++ b/fasta_formatter.xml	Tue May 08 13:25:51 2018 -0400
@@ -1,8 +1,9 @@
-<tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width">
+<tool id="cshl_fasta_formatter" version="1.0.1" name="FASTA Width">
     <description>formatter</description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
     <!--
         Note:
             fasta_formatter also has a tabular output mode (-t),
@@ -12,18 +13,18 @@
             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>
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fasta_formatter
+-w $width
+-o '$output'
+    ]]></command>
     <inputs>
-        <param format="fasta" name="input" type="data" label="Library to re-format" />
+        <expand macro="fasta_input" />
 
         <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" />
+        <data name="output" format="fasta" metadata_source="input" />
     </outputs>
     <tests>
         <test>
@@ -39,7 +40,7 @@
             <output name="output" file="fasta_formatter2.out" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 This tool re-formats a FASTA file, changing the width of the nucleotides lines.
@@ -85,5 +86,6 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
+    ]]></help>
+    <expand macro="citations" />
 </tool>