<tool id="rapsodyn_stats_mapping" name="rapsodyn_stats_mapping" version="0.01">
<description>Stats on the mapping</description>
<command interpreter="perl">
    rapsodyn_stats_mapping.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_read1_trimmednoN_file $input_read2_trimmednoN_file $input_sam_row_file $input_sam_filtered_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_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED file from your history"/>
<param name="input_read2_trimmed_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED file from your history"/>
<param name="input_read1_trimmednoN_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED noN file from your history"/>
<param name="input_read2_trimmednoN_file"  type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED noN file from your history"/>
<param name="input_sam_row_file"  type="data" format="sam" label="Select a suitable input SAM file from your history"/>
<param name="input_sam_filtered_file"  type="data" format="sam" label="Select a suitable input SAM FILTERED file from your history"/>
</inputs>
<outputs>
 <data name="output_file" format="txt" label="STATS"/>
</outputs>


<help>

</help>
</tool>