<tool id="FastQC_Summary" name="FastQC Summary" version="1.2">
  <description>Provide a one line summary of a FastQC report(s)</description>
  <requirements>
    <requirement type="package" version="1.6.924">perl-bioperl</requirement>
    <requirement type="package" version="2.49">perl-getopt-long</requirement>    
  </requirements>  
  <command detect_errors="exit_code"><![CDATA[        

    perl $__tool_directory__/fastqc_stats.pl


    #if $single_or_mate.library_type == "single"
      --fastq_se $single_or_mate.fastq_file --g_rawdata_se $rawdata_file
      --sample "$single_or_mate.fastq_file.name"
    #elif $single_or_mate.library_type == "paired"
      --fastq_pe_1 $single_or_mate.forward_fastq --fastq_pe_2 $single_or_mate.reverse_fastq --g_rawdata_pe_1 $single_or_mate.forward_rawdata --g_rawdata_pe_2 $single_or_mate.reverse_rawdata
      --sample "$single_or_mate.forward_fastq.name"
   #else
      --fastq_pe_1 $single_or_mate.fastq_collection.forward --fastq_pe_2 $single_or_mate.fastq_collection.reverse --g_rawdata_pe_1 $single_or_mate.fastqc_collection.forward --g_rawdata_pe_2 $single_or_mate.fastqc_collection.reverse
      --sample "$single_or_mate.fastq_collection.name"
    #end if
    
 

    #if $ref_or_num.select == "reference"
      --ref $ref_or_num.ref_file
    #else
      --num_bps $ref_or_num.bp_num
    #end if
    -o $out_file
    
    ]]></command>            
  <inputs>
    <conditional name="single_or_mate">
      <param name="library_type" type="select" label="Is this library single or paired-end?">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
        <option value="collection">Collection Paired-end Fastqs</option>
      </param>
      <when value="single">
	<param name="fastq_file" type="data" format="fastqsanger,fastq" label="Single end FASTQ"/>
	<param name="rawdata_file" type="data" format="txt" label="FastQC RawData"/>
      </when>
      <when value="paired">  
        <param name="forward_fastq" type="data" format="fastqsanger,fastq" label="Forward FASTQ"/>
        <param name="reverse_fastq" type="data" format="fastqsanger,fastq" label="Reverse FASTQ"/>
        <param name="forward_rawdata" type="data" format="txt" label="FASTQC forward RawData"/>
        <param name="reverse_rawdata" type="data" format="txt" label="FASTQC reverse RawData"/>
      </when>
      <when value="collection">
        <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="txt" collection_type="paired" />
        <param name="fastqc_collection" type="data_collection" label="Paired-end FastQC collection" help="" optional="false" format="txt" collection_type="paired" />
      </when>
    </conditional>
    <conditional name="ref_or_num">
      <param name="select" type="select" label="Reference file or number of base pairs?">
	<option value="reference">Reference file</option>
	<option value="num_pairs">Number of base pairs</option>
      </param>
      <when value="reference">
	<param name="ref_file" type="data" format='fasta' help="To determine raw genome coverage." label="Reference file"/>
      </when>
      <when value="num_pairs">
	<param name="bp_num" type="integer" value="" label="Number of base pairs"/>
      </when>
    </conditional>
  </inputs>
  <outputs>
    <data format="tabular" name="out_file" label="Output csv file"/>
  </outputs>
  <tests>
    <test>
      <param name="fastq_file" value="forward.fastq"/>
      <param name="rawdata_file" value="forward.txt"/>
      <param name="ref_file" value="reference_1K.fa"/>
      <output name="out_file" value="output_single.tsv"/>
    </test>
    <test>
      <param name="library_type" value="paired"/>
      <param name="forward_fastq" value="forward.fastq"/>
      <param name="reverse_fastq" value="reverse.fastq"/>
      <param name="forward_rawdata" value="forward.txt"/>
      <param name="reverse_rawdata" value="reverse.txt"/>
      <param name="ref_file" value="reference_1K.fa"/>
      <output name="out_file" value="output_pe.tsv"/>
    </test>
  </tests>
  <help>
    
What it does
============
This script provides a one line summary of the FastQC report.

Inputs
======
- **Is this library single or paired end?**: Choose Single-end or Paired-end. This option will display the correct number of input fields depending on the option selected
- **Fastq input**: - Fastqc file
- **FastQC rawData input**: - This is the txt file produced by the FastQC tool
- **Sample Name**: Sample name that will appear in the output file
- **Reference file or number of base pairs?**: Choose between providing a reference file or providing a number of basepairs to determine the raw genome coverage.

Outputs
=======
- **Output csv file**: Summarizes the FastQC report in a csv format
  </help>
</tool>