--- a/picard_FastqToSam.xml	Sat Jan 15 12:39:30 2022 +0000
+++ b/picard_FastqToSam.xml	Sun Mar 20 14:06:40 2022 +0000
@@ -1,8 +1,8 @@
-<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
+<tool name="FastqToSam" id="picard_FastqToSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="20.01">
     <description>convert Fastq data into unaligned BAM</description>
     <macros>
         <import>picard_macros.xml</import>
-        <token name="@WRAPPER_VERSION@">1</token>
+        <token name="@WRAPPER_VERSION@">2</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">picard_fastqtosam</xref>
@@ -10,20 +10,45 @@
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
     @java_options@
+    #if str( $input_type.input_type_selector ) == "se":
+      #set fwd = $input_type.fastq
+      #set rev = None
+    #elif str( $input_type.input_type_selector ) == "pe":
+      #set fwd = $input_type.fastq
+      #set rev = $input_type.fastq2
+    #else
+      #set fwq = $input_type.fastq.forward
+      #set rev = $input_type.fastq.reverse
+    #end if
+
+    #if $fwd.ext.endswith(".gz")
+      gunzip -c '$fwd' > fwd.fastq &&
+    #else
+      ln -s '$fwd' fwd.fastq &&
+    #end if
+    #if rev
+      #if rev.ext.endswith(".gz")
+        gunzip -c '$rev' > rev.fastq &&
+      #else
+        ln -s '$rev' rev.fastq &&
+      #end if
+    #end if
+   
     picard
     FastqToSam
 
-    #if str( $input_type.input_type_selector ) == "se":
-      FASTQ="${input_type.fastq}"
-    #elif str( $input_type.input_type_selector ) == "pe":
-      FASTQ="${input_type.fastq}"
-      FASTQ2="${input_type.fastq2}"
-    #else
-      FASTQ="${input_type.fastq.forward}"
-      FASTQ2="${input_type.fastq.reverse}"
+    FASTQ=fwd.fastq
+    #if rev
+      FASTQ2=rev.fastq
     #end if
 
-    QUALITY_FORMAT="${quality_format}"
+    #if $fwd.ext.startswith("fastqillumina")
+      QUALITY_FORMAT="Illumina"
+    #else if $fwd.ext.startswith("fastqsolexa")
+      QUALITY_FORMAT="Solexa"
+    #else 
+      QUALITY_FORMAT="Standard"
+    #end if
     OUTPUT="${outFile}"
     READ_GROUP_NAME="${read_group_name}"
     SAMPLE_NAME="${sample_name}"
@@ -79,23 +104,17 @@
         <option value="pc">Paired collection</option>
       </param>
       <when value="se">
-        <param name="fastq" type="data" format="fastq" label="Input fastq file for single end data" help="FASTQ"/>
+        <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for single end data" help="FASTQ"/>
       </when>
       <when value="pe">
-        <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
-        <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
+        <param name="fastq" type="data" format="fastq,fastq.gz" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
+        <param name="fastq2" type="data" format="fastq,fastq.gz" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
       </when>
       <when value="pc">
-        <param name="fastq" type="data_collection" collection_type="paired" format="fastq" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
+        <param name="fastq" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
       </when>
     </conditional>
 
-    <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
-      <option value="Standard" selected="True">Sanger (+33)</option>
-      <option value="Illumina">Illumina (+64)</option>
-      <option value="Solexa">Solexa (+66)</option>
-    </param>
-
     <param name="read_group_name" type="text" value="A" label="Read group name" help="READ_GROUP_NAME"/>
     <param name="sample_name" type="text" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
     <param name="library_name" type="text" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
@@ -117,13 +136,12 @@
   </inputs>
 
   <outputs>
-    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
+    <data format="unsorted.bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
   </outputs>
 
   <tests>
     <test>
       <param name="input_type_selector" value="pe" />
-      <param name="quality_format" value="Standard" />
       <param name="read_group_name" value="A" />
       <param name="sample_name" value="sample-a" />
       <param name="library_name" value="A"/>
@@ -139,9 +157,9 @@
       <param name="strip_unpairied_mate_number" value="False" />
       <param name="allow_and_ignore_empty_lines" value="False" />
       <param name="validation_stringency" value="LENIENT"/>
-      <param name="fastq" value="picard_FastqToSam_read1.fq" ftype="fastq" />
-      <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" />
-      <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/>
+      <param name="fastq" value="picard_FastqToSam_read1.fq.gz" ftype="fastq.gz" />
+      <param name="fastq2" value="picard_FastqToSam_read2.fq.gz" ftype="fastq.gz" />
+      <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="unsorted.bam" lines_diff="4"/>
     </test>
   </tests>