--- a/convert.xml	Wed Feb 11 09:26:43 2015 -0500
+++ b/convert.xml	Thu Jun 04 17:52:04 2015 +0200
@@ -6,6 +6,12 @@
   <expand macro="requirements"/>
   <version_command>mimodd version -q</version_command>
   <command>
+  #if $str($mode.split_on_rgs) or $str($mode.oformat)=="fastq" or $str($mode.oformat)=="gz":
+    echo "Your input data is now getting processed by MiModD. The output will be split into several files based on the read groups found in the input.\nThis history item will remain in the busy state until the job is finished.\nAfter the job is showing as finished, Galaxy will start adding the results files to your history one by one.\n\nThis may take a while to complete! \n\nYou should refresh your history to see if new files have arrived.\n\nThis message is for your information only and can be deleted from the history once the job has finished." > $output_split_on_read_groups;
+
+    mkdir converted_data;
+  #end if
+  
 	mimodd convert 
  
   	#for $i in $mode.input_list
@@ -17,30 +23,37 @@
 	#if $str($mode.header) != "None":  	
 		--header "$(mode.header)"
 	#end if
-	--ofile "$outputname"
+
+	#if $str($outputname) == "None":
+	  --ofile converted_data/read_group
+	#else
+	  --ofile "$outputname"
+	#end if
 	--iformat $(mode.iformat)
 	--oformat $(mode.oformat)
+	${mode.split_on_rgs}
   </command>
   
   <inputs>
     <conditional name="mode">
-	<param name="iformat" type="select" label="input file format" help="Your choice will update the interface to display further choices appropriate for your type of input data.">
+	  <param name="iformat" type="select" label="input file format" help="Your choice will update the interface to display further choices appropriate for your type of input data.">
 	    <option value="fastq">fastq: single-end (one file)</option>
 	    <option value="fastq_pe">fastq: paired-end (two files)</option>
 	    <option value="gz">gzip compressed fastq: single-end (one file)</option>
 	    <option value="gz_pe">gzip compressed fastq: paired-end (two files)</option>
 	    <option value="sam">sam</option>
 	    <option value="bam">bam</option>
-        </param>	
-            <when value="fastq">
+      </param>	
+        <when value="fastq">
 	      <param name="oformat" type="select" label="output file format">
 	        <option value="sam">sam</option>
 	        <option value="bam">bam</option>
 	      </param>
-	    <repeat name="input_list" title="fastq input dataset" default="1" min="1">
-		<param name="file1" format="fastq" type="data" label="inputfile"/>
-	    </repeat>
-        <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>	    
+	      <repeat name="input_list" title="fastq input dataset" default="1" min="1">
+		    <param name="file1" format="fastq" type="data" label="inputfile"/>
+	      </repeat>
+          <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
+          <param name="split_on_rgs" type="hidden" value=""/>	    
 	    </when>
 	    <when value="fastq_pe">
 	      <param name="oformat" type="select" label="output file format">
@@ -48,20 +61,22 @@
 	        <option value="bam">bam</option>
 	      </param>
 	      <repeat name="input_list" title="fastq input datasets" default="1" min="1">
-		  <param format="fastq" name="file1" type="data" label="inputfile with the first set of reads of paired-end data"/>		
-		  <param format="fastq" name="file2" type="data" label="inputfile with the second set of reads of paired-end data"/>
+		    <param format="fastq" name="file1" type="data" label="inputfile with the first set of reads of paired-end data"/>		
+		    <param format="fastq" name="file2" type="data" label="inputfile with the second set of reads of paired-end data"/>
 	      </repeat>
           <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
+          <param name="split_on_rgs" type="hidden" value=""/>
 	    </when>
         <when value="gz">
 	      <param name="oformat" type="select" label="output file format">
 	        <option value="sam">sam</option>
 	        <option value="bam">bam</option>
 	      </param>
-	    <repeat name="input_list" title="fastq.gz input dataset" default="1" min="1">
-		<param name="file1" format="data" type="data" label="inputfile"/>
-	    </repeat>
-        <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
+	      <repeat name="input_list" title="fastq.gz input dataset" default="1" min="1">
+		    <param name="file1" format="data" type="data" label="inputfile"/>
+	      </repeat>
+          <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
+          <param name="split_on_rgs" type="hidden" value=""/>
 	    </when>
 	    <when value="gz_pe">
 	      <param name="oformat" type="select" label="output file format">
@@ -69,37 +84,56 @@
 	        <option value="bam">bam</option>
 	      </param>
 	      <repeat name="input_list" title="fastq.gz input datasets" default="1" min="1">
-		<param format="data" name="file1" type="data" label="inputfile with the first set of reads of paired-end data"/>		
-		<param format="data" name="file2" type="data" label="inputfile with the second set of reads of paired-end data"/>
-	    </repeat>
-        <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
+		    <param format="data" name="file1" type="data" label="inputfile with the first set of reads of paired-end data"/>		
+		    <param format="data" name="file2" type="data" label="inputfile with the second set of reads of paired-end data"/>
+	      </repeat>
+          <param name="header" type="data" format="sam" label="Use Header File" help="A SAM file with header information, as generated, for example, by the NGS Run Annotation Tool, that will be used to attach metainformation to the results file."/>
+          <param name="split_on_rgs" type="hidden" value=""/>
 	    </when>
 	    <when value="sam">
 	      <param name="oformat" type="select" label="output file format">
 	        <option value="bam">bam</option>
+	        <option value="sam">sam</option>
+	        <option value="fastq">fastq</option>
+	        <option value="gz">gzipped fastq</option>
 	      </param>
 	      <repeat name="input_list" title="sam input dataset" default="1" min="1" max="1">
-		<param name="file1" format="sam" type="data" label="inputfile"/>
-	    </repeat>
-	    <param name="header" type="hidden" value="None"/>
+		    <param name="file1" format="sam" type="data" label="inputfile"/>
+	      </repeat>
+	      <param name="header" type="hidden" value="None"/>
+	      <param name="split_on_rgs" type="boolean" truevalue="--split-on-rgs" falsevalue="" checked="false" label="Split output based on read group IDs" help="If the input file contains reads from different read groups, write them to separate output files; implied automatically for conversions to fastq and gzipped fastq format"/>
 	    </when>
 	    <when value="bam">
 	      <param name="oformat" type="select" label="output file format">
 	        <option value="sam">sam</option>
+	        <option value="bam">bam</option>
+	        <option value="fastq">fastq</option>
+	        <option value="gz">gzipped fastq</option>
 	      </param>
 	      <repeat name="input_list" title="bam input dataset" default="1" min="1" max="1">
-		<param name="file1" format="bam" type="data" label="inputfile"/>
-	    </repeat>
-	    <param name="header" type="hidden" value="None"/>
+		    <param name="file1" format="bam" type="data" label="inputfile"/>
+	      </repeat>
+	      <param name="header" type="hidden" value="None"/>
+	      <param name="split_on_rgs" type="boolean" truevalue="--split-on-rgs" falsevalue="" checked="false" label="Split output based on read group IDs" help="If the input file contains reads from different read groups, write them to separate output files; implied automatically for conversions to fastq and gzipped fastq format"/>
 	    </when>
     </conditional>
   </inputs>
   
   <outputs>
     <data name="outputname" format="bam" label="Converted reads from MiModd ${tool.name} on ${on_string}">
-	<change_format>
-	    <when input="mode.oformat" value="sam" format="sam" />
-	</change_format>
+	  <change_format>
+	      <when input="mode.oformat" value="sam" format="sam" />
+	  </change_format>
+	  <filter>
+	    (not mode['split_on_rgs'] and mode['oformat'] not in ("fastq", "gz"))
+	  </filter>
+    </data>
+    
+    <data name="output_split_on_read_groups" format="txt" label="MiModD ${tool.name} run on ${on_string}">
+	  <filter>
+	    (mode['split_on_rgs'] or mode['oformat'] in ("fastq", "gz"))
+	  </filter>
+	  <discover_datasets pattern="__designation_and_ext__" directory="converted_data" visible="true" />
     </data>
   </outputs>
 
@@ -114,7 +148,7 @@
 
 **Notes:**
 
-1) In its standard configuration Galaxy will decompress any .gz files during their upload, so the option to align gzipped fastq input is useful only with customized Galaxy instances or by using linked files as explained in our `recipe for using gzipped fastq files in Galaxy`_ from the `MiModD user guide`_.
+1) In its standard configuration Galaxy will decompress any .gz files during their upload, so the option to convert gzipped fastq input is useful only with customized Galaxy instances or by using linked files as explained in our `recipe for using gzipped fastq files in Galaxy`_ from the `MiModD user guide`_.
 
 2) The tool can convert fastq files representing data from paired-end sequencing runs to appropriate SAM/BAM format provided that the mate information is split over two fastq files in corresponding order.