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1 <tool id="rapsodyn_stats" name="rapsodyn_stats" version="0.01">
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2 <description>Merge best results from Blast</description>
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3 <command interpreter="perl">
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4 rapsodyn_stats.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 $input_mpileup_row_file $input_mpileup_filtered_file $input_list_filtered_file $input_blast_filtered_file > $output_file
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5 </command>
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6 <inputs>
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7 <param name="input_read1_row_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 ROW file from your history"/>
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8 <param name="input_read2_row_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 ROW file from your history"/>
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9 <param name="input_read1_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ1 TRIMMED file from your history"/>
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10 <param name="input_read2_trimmed_file" type="data" format="fastq,fastqsanger,fastqsolexa,fastqillumina" label="Select a suitable input READ2 TRIMMED file from your history"/>
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11 <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"/>
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12 <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"/>
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13 <param name="input_sam_row_file" type="data" format="sam" label="Select a suitable input SAM file from your history"/>
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14 <param name="input_sam_filtered_file" type="data" format="sam" label="Select a suitable input SAM FILTERED file from your history"/>
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15 <param name="input_mpileup_row_file" type="data" format="pileup" label="Select a suitable input MPILEUP file from your history"/>
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16 <param name="input_mpileup_filtered_file" type="data" format="pileup" label="Select a suitable input MPILEUP FILTERED file from your history"/>
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17 <param name="input_list_filtered_file" type="data" format="pileup" label="Select a suitable input LIST FILTERED file from your history"/>
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18 <param name="input_blast_filtered_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED file from your history"/>
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19 </inputs>
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20 <outputs>
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21 <data name="output_file" format="txt" label="STATS"/>
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22 </outputs>
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23
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24
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25 <help>
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26
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27 </help>
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28 </tool>
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