diff fastx_artifacts_filter.xml @ 3:dd3737e40dce draft

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

--- a/fastx_artifacts_filter.xml	Wed Nov 11 12:38:23 2015 -0500
+++ b/fastx_artifacts_filter.xml	Tue May 08 13:27:02 2018 -0400
@@ -1,22 +1,21 @@
-<tool id="cshl_fastx_artifacts_filter" version="1.0.0" name="Remove sequencing artifacts">
+<tool id="cshl_fastx_artifacts_filter" version="1.0.1" name="Remove sequencing artifacts">
     <description></description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-zcat -f < '$input' | fastx_artifacts_filter -v -o '$output'
-#if $input.ext == "fastqsanger":
-    -Q 33
-#end if
-]]>
-    </command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_artifacts_filter
+-v
+-o '$output'
+@FQQUAL@
+    ]]></command>
 
     <inputs>
-        <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to filter" />
+        <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>
@@ -30,7 +29,7 @@
             <output name="output" ftype="fastqsanger" file="fastx_artifacts2.out" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 This tool filters sequencing artifacts (reads with all but 3 identical bases).
@@ -87,6 +86,7 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
+    ]]></help>
+    <expand macro="citations" />
 <!-- FASTX-Artifacts-filter is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->
 </tool>