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2
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1 <tool id="rapsosnp_stats4x" name="rapsosnp_stats4x" version="0.01">
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2 <description>Stats for rapsosnp workflow</description>
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3 <command interpreter="perl">
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4 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
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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
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10 <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"/>
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11 <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"/>
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12 <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"/>
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13 <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"/>
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14 <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"/>
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15 <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"/>
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16 <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"/>
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17 <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"/>
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18
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19 <param name="input_sam_row_part1_file" type="data" format="sam" label="Select a suitable input SAM PART1 file from your history"/>
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20 <param name="input_sam_row_part2_file" type="data" format="sam" label="Select a suitable input SAM PART2 file from your history"/>
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21 <param name="input_sam_row_part3_file" type="data" format="sam" label="Select a suitable input SAM PART3 file from your history"/>
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22 <param name="input_sam_row_part4_file" type="data" format="sam" label="Select a suitable input SAM PART4 file from your history"/>
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23 <param name="input_sam_filtered_part1_file" type="data" format="sam" label="Select a suitable input SAM PART1 FILTERED file from your history"/>
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24 <param name="input_sam_filtered_part2_file" type="data" format="sam" label="Select a suitable input SAM PART2 FILTERED file from your history"/>
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25 <param name="input_sam_filtered_part3_file" type="data" format="sam" label="Select a suitable input SAM PART3 FILTERED file from your history"/>
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26 <param name="input_sam_filtered_part4_file" type="data" format="sam" label="Select a suitable input SAM PART4 FILTERED file from your history"/>
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27
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28
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29 <param name="input_mpileup_variant_file" type="data" format="pileup" label="Select a suitable input MPILEUP VARIANT file from your history"/>
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30 <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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31
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32 <param name="input_blast_filtered_part1_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART1 file from your history"/>
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33 <param name="input_blast_filtered_part2_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART2 file from your history"/>
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34 <param name="input_blast_filtered_part3_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART3 file from your history"/>
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35 <param name="input_blast_filtered_part4_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART4 file from your history"/>
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36
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37 <param name="input_snp_selected_file" type="data" format="pileup" label="Select a suitable input SNP SELECTED file from your history"/>
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38 </inputs>
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39 <outputs>
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40 <data name="output_file" format="txt" label="STATS"/>
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41 </outputs>
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42
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43
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44 <help>
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45
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46 </help>
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47 </tool>
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