<tool id="load_multiFASTQFiles" name="load_multiFASTQfiles" >
  <description>To load several FASTQ files from different conditions.</description>
  <command interpreter="python"> loadMultiFastqFiles.py -o $multiFASTQfiles_out
#if $single_end_paired_end.mapping_mode == 'single':
	-i
	#for $i in $single_end_paired_end.condition_groups
	#for $j in $i.replicates
	$j.fastq_file
	#end for
	@
	#end for

#elif $single_end_paired_end.mapping_mode == 'paired':

	--pairedEnd $multiFASTQfiles_paired_end_out
	-i
	#for $i in $single_end_paired_end.condition_groups
	#for $j in $i.replicates
	$j.fastq_file
	@@
	$j.fastq_paired_end_file
	#end for
	@
	#end for
#end if

</command>
  <inputs>
		  <conditional name="single_end_paired_end">
			   <param name="mapping_mode" type="select" label="The uploading fastq files for single-end or paired-end mapping mode.">
				<option value="single">Single-End</option>
				<option value="paired">Paire-End</option>
			   </param>
	           <when value="single">
	  		<repeat name="condition_groups" title="Condition group" min="2">
   		   	<repeat name="replicates" title="Replicate">
		        <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/>
     		   </repeat>
     		   </repeat>
		   </when>
		   <when value="paired">
	  		<repeat name="condition_groups" title="Condition group" min="2">
      		   	<repeat name="replicates" title="Replicate">
		        <param name="fastq_file" format="fastq" type="data" label="FASTQ file. Can show the sequences quality."/>
		        <param name="fastq_paired_end_file" format="fastq" type="data" label="fastq paired end complementary file" help="Add the corresponding paired end file for paired end mapping"/>
     		   </repeat>
     		   </repeat>
		   </when>
	
 		   </conditional>
  </inputs>

  <outputs>
    <data format="txt" name="multiFASTQfiles_out" label="loadMultiFASTQFiles result" help="This program gives you a list of files you choose for the following data analysis."/>
    <data format="txt" name="multiFASTQfiles_paired_end_out" label="loadMultiFASTQFiles for paired end result" help="This program gives you a list of files you choose for the following data analysis.">
	    <filter>(single_end_paired_end['mapping_mode']=='paired')</filter>

    </data>
</outputs>
<help>
	**This tool is to help upload several data for differential expression pipeline. Before click 'Execute', you should Click** Ctrl + here_ **first to open the pipeline in a new page.**

	.. _here: http://127.0.0.1:8085/u/yufei-luo/w/differentialexpressiondeseq-with-replicates 
</help>

</tool>