diff fastq_quality_converter.xml @ 2:0b7eccecaa34 draft

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

--- a/fastq_quality_converter.xml	Tue Oct 13 12:39:43 2015 -0400
+++ b/fastq_quality_converter.xml	Tue May 08 12:49:47 2018 -0400
@@ -1,60 +1,65 @@
-<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.0">
+<tool id="cshl_fastq_quality_converter" name="Quality format converter" version="1.0.1">
     <description>(ASCII-Numeric)</description>
-    <requirements>
-        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
-    </requirements>
-    <command>
-<![CDATA[
-zcat -f < '$input' | fastq_quality_converter $QUAL_FORMAT -o '$output' -Q $offset
-]]>
-    </command>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+@CATS@ fastq_quality_converter
+$QUAL_FORMAT
+-o '$output'
+@FQQUAL@
+    ]]></command>
     <inputs>
-        <param format="fastq" name="input" type="data" label="Library to convert" />
+        <expand macro="fastq_input" />
 
         <param name="QUAL_FORMAT" type="select" label="Desired output format">
             <option value="-a">ASCII (letters) quality scores</option>
             <option value="-n">Numeric quality scores</option>
         </param>
-
-        <param name="offset" type="select" label="FASTQ ASCII offset">
-            <option value="33">33</option>
-            <option selected="true" value="64">64</option>
-        </param>
     </inputs>
     <outputs>
-        <data format="fastq" name="output" metadata_source="input" />
+        <data name="output" format="fastq" metadata_source="input" />
     </outputs>
     <tests>
         <test>
             <!-- ASCII to NUMERIC -->
-            <param name="input" value="fastq_qual_conv1.fastq" />
+            <param name="input" ftype="fastqillumina" value="fastq_qual_conv1.fastq" />
             <param name="QUAL_FORMAT" value="Numeric quality scores" />
-            <param name="offset" value="64" />
             <output name="output" file="fastq_qual_conv1.out" />
         </test>
         <test>
-            <!-- ASCII to ASCII (basically, a no-op, but it should still produce a valid output -->
-            <param name="input" value="fastq_qual_conv1.fastq" />
+            <!-- ASCII to ASCII (should basically copy the input to the output unchanged) -->
+            <param name="input" ftype="fastqillumina" value="fastq_qual_conv1.fastq" />
             <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
-            <param name="offset" value="64" />
             <output name="output" file="fastq_qual_conv1a.out" />
         </test>
         <test>
             <!-- NUMERIC to ASCII -->
-            <param name="input" value="fastq_qual_conv2.fastq" />
+            <param name="input" ftype="fastqillumina" value="fastq_qual_conv2.fastq" />
             <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
-            <param name="offset" value="64" />
             <output name="output" file="fastq_qual_conv2.out" />
         </test>
         <test>
-            <!-- NUMERIC to NUMERIC (basically, a no-op, but it should still produce a valid output -->
-            <param name="input" value="fastq_qual_conv2.fastq" />
+            <!-- NUMERIC to NUMERIC (should basically copy the input to the output unchanged) -->
+            <param name="input" ftype="fastqillumina" value="fastq_qual_conv2.fastq" />
             <param name="QUAL_FORMAT" value="Numeric quality scores" />
-            <param name="offset" value="64" />
             <output name="output" file="fastq_qual_conv2n.out" />
         </test>
+        <test>
+            <!-- ASCII to NUMERIC -->
+            <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in5.fastq" />
+            <param name="QUAL_FORMAT" value="Numeric quality scores" />
+            <output name="output" file="fastq_quality_converter-out5.fastq" />
+        </test>
+        <test>
+            <!-- ASCII to ASCII (should basically copy the input to the output unchanged) -->
+            <param name="input" ftype="fastqsanger" value="fastq_quality_converter-in6.fastq" />
+            <param name="QUAL_FORMAT" value="ASCII (letters) quality scores" />
+            <output name="output" file="fastq_quality_converter-out6.fastq" />
+        </test>
     </tests>
-    <help>
+    <help><![CDATA[
 **What it does**
 
 Converts a Solexa FASTQ file to/from numeric or ASCII quality format.
@@ -93,6 +98,7 @@
 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
 
  .. __: http://hannonlab.cshl.edu/fastx_toolkit/
-    </help>
+    ]]></help>
+    <expand macro="citations" />
 <!-- FASTQ-Quality-Converter is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->
 </tool>