<tool id="rapsosnp_stats4x" name="rapsosnp_stats4x" version="0.01">
<description>Stats for rapsosnp workflow</description>
<command interpreter="perl">
    rapsosnp_stats4x.pl $input_read1_row_file $input_read2_row_file $input_read1_part1_trimmed_file $input_read1_part2_trimmed_file $input_read1_part3_trimmed_file $input_read1_part4_trimmed_file $input_read2_part1_trimmed_file $input_read2_part2_trimmed_file $input_read2_part3_trimmed_file $input_read2_part4_trimmed_file $input_sam_row_part1_file $input_sam_row_part2_file $input_sam_row_part3_file $input_sam_row_part4_file $input_sam_filtered_part1_file $input_sam_filtered_part2_file $input_sam_filtered_part3_file $input_sam_filtered_part4_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_part1_file $input_blast_filtered_part2_file $input_blast_filtered_part3_file $input_blast_filtered_part4_file $input_snp_selected_file  > $output_file 
</command>
<inputs>
<param name="input_read1_row_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 ROW file from your history"/>
<param name="input_read2_row_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 ROW file from your history"/>

<param name="input_read1_part1_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART1 TRIMMED file from your history"/>
<param name="input_read1_part2_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART2 TRIMMED file from your history"/>
<param name="input_read1_part3_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART3 TRIMMED file from your history"/>
<param name="input_read1_part4_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 PART4 TRIMMED file from your history"/>
<param name="input_read2_part1_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART1 TRIMMED file from your history"/>
<param name="input_read2_part2_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART2 TRIMMED file from your history"/>
<param name="input_read2_part3_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART3 TRIMMED file from your history"/>
<param name="input_read2_part4_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 PART4 TRIMMED file from your history"/>

<param name="input_sam_row_part1_file"  type="data" format="sam" label="Select a suitable input SAM PART1 file from your history"/>
<param name="input_sam_row_part2_file"  type="data" format="sam" label="Select a suitable input SAM PART2 file from your history"/>
<param name="input_sam_row_part3_file"  type="data" format="sam" label="Select a suitable input SAM PART3 file from your history"/>
<param name="input_sam_row_part4_file"  type="data" format="sam" label="Select a suitable input SAM PART4 file from your history"/>
<param name="input_sam_filtered_part1_file"  type="data" format="sam" label="Select a suitable input SAM PART1 FILTERED file from your history"/>
<param name="input_sam_filtered_part2_file"  type="data" format="sam" label="Select a suitable input SAM PART2 FILTERED file from your history"/>
<param name="input_sam_filtered_part3_file"  type="data" format="sam" label="Select a suitable input SAM PART3 FILTERED file from your history"/>
<param name="input_sam_filtered_part4_file"  type="data" format="sam" label="Select a suitable input SAM PART4 FILTERED file from your history"/>


<param name="input_mpileup_variant_file"  type="data" format="pileup" label="Select a suitable input MPILEUP VARIANT file from your history"/>
<param name="input_list_filtered_file"  type="data" format="pileup" label="Select a suitable input LIST FILTERED file from your history"/>

<param name="input_blast_filtered_part1_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART1 file from your history"/>
<param name="input_blast_filtered_part2_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART2 file from your history"/>
<param name="input_blast_filtered_part3_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART3 file from your history"/>
<param name="input_blast_filtered_part4_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART4 file from your history"/>

<param name="input_snp_selected_file"  type="data" format="pileup" label="Select a suitable input SNP SELECTED file from your history"/>
</inputs>
<outputs>
 <data name="output_file" format="txt" label="STATS"/>
</outputs>


<help>

</help>
</tool>