--- a/qfilt.xml	Mon Jun 18 16:55:03 2018 -0400
+++ b/qfilt.xml	Sun Apr 18 20:35:13 2021 +0000
@@ -1,11 +1,11 @@
-<?xml version="1.0"?>
-<tool id="qfilt" version="1.0.0" name="qfilt">
+<tool id="qfilt" version="1.0.0+galaxy1" name="qfilt" profile="20.01">
     <description>filter sequencing data using simple heuristics</description>
     <requirements>
         <requirement type="package" version="0.0.1">qfilt</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         qfilt -o '$filtered_output'
+        -f $output_format
         #if str($options.advanced) == 'advanced':
             -q $options.qscore
             -l $options.length
@@ -20,11 +20,15 @@
                 -t $options.mismatch
                 -T '$options.prefix'
             #end if
-            -f $options.output_format
             $options.tolerate_homopolymeric $options.tolerate_ambiguous
         #end if
         #if $input_data.format == 'fastq':
-            -Q '$input_data.fastq'
+            -Q 
+            #if $input_data.fastq.ext.endswith('.gz')
+                <(zcat '$input_data.fastq')
+            #else
+                '$input_data.fastq'
+            #end if
         #else:
             -F '$input_data.fasta'
             '$input_data.qual'
@@ -37,7 +41,7 @@
                 <option value="fastaq">FASTA+QUAL</option>
             </param>
             <when value="fastq">
-                <param name="fastq" argument="-Q" type="data" format="fastq" label="Input FASTA" help="FASTQ File" />
+                <param name="fastq" argument="-Q" type="data" format="fastq,fastq.gz" label="Input FASTA" help="FASTQ File" />
             </when>
             <when value="fastaq">
                 <param name="fasta" argument="-F" type="data" format="fasta" label="Input FASTA" help="FASTA File" />
@@ -62,12 +66,12 @@
                 <param name="remove" argument="-R" type="text" label="Remove" help="rather than splitting or truncating, remove reads which contain more than COUNT low quality bases this option only works in COMBINATION with the -P (punch) option" />
                 <param name="prefix" argument="-T" type="text" label="Prefix" help="if supplied, only reads with this PREFIX are retained, and the PREFIX is stripped from each contributing read" />
                 <param name="mismatch" argument="-t" type="integer" value="0" label="Mismatch" help="if PREFIX is supplied, prefix matching tolerates at most MISMATCH mismatches" />
-                <param name="output_format" argument="-f" type="select" label="Format" help="output in FASTA or FASTQ format (default=FASTA)" >
-                    <option value="FASTA">FASTA</option>
-                    <option value="FASTQ">FASTQ</option>
-                </param>
             </when>
         </conditional>
+        <param name="output_format" argument="-f" type="select" label="Format" help="output in FASTA or FASTQ format (default=FASTA)" >
+            <option value="FASTA">FASTA</option>
+            <option value="FASTQ">FASTQ</option>
+        </param>
     </inputs>
     <outputs>
         <data format="fasta" name="filtered_output">
@@ -78,21 +82,23 @@
     </outputs>
     <tests>
         <test>
-            <param name="fastq" value="qfilt-in1.fastq" />
+            <param name="fastq" value="qfilt-in1.fastq" ftype="fastq" />
             <output file="qfilt-out1.fa" ftype="fasta" name="filtered_output" />
         </test>
         <test>
             <param name="format" value="fastq" />
-            <param name="fastq" value="qfilt-in1.fastq" />
+            <param name="fastq" value="qfilt-in1.fastq.gz" ftype="fastq.gz" />
             <param name="advanced" value="advanced" />
             <param name="tolerate_homopolymeric" value="False" />
             <output file="qfilt-out2.fa" ftype="fasta" name="filtered_output" />
         </test>
         <test>
+            
             <param name="fasta" value="qfilt-in2.fa" />
             <param name="qual" value="qfilt-in2.qual" />
             <param name="format" value="fastaq" />
-            <output file="qfilt-out3.fa" ftype="fasta" name="filtered_output" />
+            <param name="output_format" value="FASTQ" />
+            <output file="qfilt-out3.fq" ftype="fastq" name="filtered_output" />
         </test>
     </tests>
     <help><![CDATA[