diff fastx_collapser.xml @ 3:7ce1891db6f5 draft

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

--- a/fastx_collapser.xml	Wed Nov 11 12:39:04 2015 -0500
+++ b/fastx_collapser.xml	Tue May 08 13:27:36 2018 -0400
@@ -1,32 +1,30 @@
-<tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse">
+<tool id="cshl_fastx_collapser" version="1.0.1" name="Collapse">
     <description>sequences</description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-zcat -f < '$input' | fastx_collapser -v -o '$output'
-#if $input.ext == "fastqsanger":
-    -Q 33
-#end if
-]]>
-    </command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastx_collapser -v
+-o '$output'
+@FQQUAL@
+    ]]></command>
 
     <inputs>
-        <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" />
+        <expand macro="fastx_input" />
     </inputs>
     <outputs>
-        <data format="fasta" name="output" metadata_source="input" />
+        <data name="output" format="fasta" metadata_source="input" />
     </outputs>
-    <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
     <tests>
         <test>
             <param name="input" value="fasta_collapser1.fasta" />
-            <param name="output" file="fasta_collapser1.out" />
+            <!-- The output is sorted differently depending on architecture,
+                 so the sort attribute is needed here -->
+            <output name="output" file="fasta_collapser1.out" sort="true" />
         </test>
     </tests>
-    -->
-    <help>
+    <help><![CDATA[
 **What it does**
 
 This tool collapses identical sequences in a FASTA file into a single sequence.
@@ -80,11 +78,11 @@
 
 means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.
 
-
 ------
 
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
+    ]]></help>
+    <expand macro="citations" />
 </tool>