diff fasta_nucleotide_changer.xml @ 3:cc9a18dd41c9 draft

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

--- a/fasta_nucleotide_changer.xml	Mon Oct 12 10:18:10 2015 -0400
+++ b/fasta_nucleotide_changer.xml	Tue May 08 13:26:01 2018 -0400
@@ -1,15 +1,17 @@
-<tool id="cshl_fasta_nucleotides_changer" version="1.0.0" name="RNA/DNA" >
+<tool id="cshl_fasta_nucleotides_changer" version="1.0.1" name="RNA/DNA" >
     <description>converter</description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-zcat -f < '$input' | fasta_nucleotide_changer -$mode -v -o '$output'
-]]>
-    </command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fasta_nucleotide_changer
+-$mode
+-v
+-o '$output'
+    ]]></command>
     <inputs>
-        <param format="fasta" name="input" type="data" label="Library to convert" />
+        <expand macro="fasta_input" />
 
         <param name="mode" type="select" label="Convert">
             <option value="d">RNA to DNA (U to T)</option>
@@ -17,7 +19,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
         <test>
@@ -31,7 +33,7 @@
             <output name="output" ftype="fasta" file="fasta_nuc_change2.out" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 This tool converts RNA FASTA files to DNA (and vice-versa).
@@ -68,5 +70,6 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
+    ]]></help>
+    <expand macro="citations" />
 </tool>