diff fastx_renamer.xml @ 2:d8a3d31554d7 draft

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

--- a/fastx_renamer.xml	Wed Nov 11 12:39:46 2015 -0500
+++ b/fastx_renamer.xml	Tue May 08 13:28:10 2018 -0400
@@ -1,19 +1,19 @@
-<tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
+<tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" >
     <description></description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v
-#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_renamer
+-n $TYPE
+-o '$output'
+-v
+@FQQUAL@
+    ]]></command>
 
     <inputs>
-        <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />
+        <expand macro="fastx_input" />
 
         <param name="TYPE" type="select" label="Rename sequence identifiers to">
             <option value="SEQ">Nucleotides sequence</option>
@@ -22,11 +22,16 @@
     </inputs>
 
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
+        <test>
+            <param name="input" value="fastx_renamer-in1.fastq" />
+            <param name="TYPE" value="SEQ" />
+            <output name="output" file="fastx_renamer-out1.fastq" />
+        </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 This tool renames the sequence identifiers in a FASTQ/A file.
@@ -65,6 +70,6 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
-<!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->
+    ]]></help>
+    <expand macro="citations" />
 </tool>