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view rapsodyn/rapsosnp_stats.xml @ 1:7f36bd129321 draft

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author mcharles
date Wed, 10 Sep 2014 10:24:01 -0400
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<tool id="rapsosnp_stats" name="rapsosnp_stats" version="0.01">
<description>Merge best results from Blast</description>
<command interpreter="perl">
    rapsosnp_stats.pl $input_read1_row_file $input_read2_row_file $input_read1_trimmed_file $input_read2_trimmed_file $input_sam_row_file $input_sam_filtered_file $input_mpileup_variant_file $input_list_filtered_file $input_blast_filtered_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_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_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"/>
<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_file"  type="data" format="pileup" label="Select a suitable input BLAST FILTERED 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>