diff fastx_reverse_complement.xml @ 3:9d06c848a628 draft

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

--- a/fastx_reverse_complement.xml	Tue Oct 13 12:41:59 2015 -0400
+++ b/fastx_reverse_complement.xml	Tue May 08 12:52:49 2018 -0400
@@ -1,21 +1,19 @@
-<tool id="cshl_fastx_reverse_complement" version="1.0.0" name="Reverse-Complement">
+<tool id="cshl_fastx_reverse_complement" version="1.0.1" name="Reverse-Complement">
     <description></description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-zcat -f < '$input' | fastx_reverse_complement -v -o '$output'
-#if $input.ext == "fastqsanger":
-    -Q 33
-#end if
-]]>
-    </command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_reverse_complement -v
+-o '$output'
+@FQQUAL@
+    ]]></command>
     <inputs>
-        <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
+        <expand macro="fastx_input" />
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
         <test>
@@ -29,7 +27,7 @@
             <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 This tool reverse-complements each sequence in a library.
@@ -59,5 +57,6 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
+    ]]></help>
+    <expand macro="citations" />
 </tool>