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comparison rapsodyn/rapsosnp_stats4x.xml @ 2:761fecc07fa9 draft

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author mcharles
date Thu, 11 Sep 2014 03:10:47 -0400
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1:7f36bd129321 2:761fecc07fa9
1 <tool id="rapsosnp_stats4x" name="rapsosnp_stats4x" version="0.01">
2 <description>Stats for rapsosnp workflow</description>
3 <command interpreter="perl">
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
5 </command>
6 <inputs>
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"/>
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"/>
9
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"/>
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"/>
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"/>
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"/>
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"/>
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"/>
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"/>
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"/>
18
19 <param name="input_sam_row_part1_file" type="data" format="sam" label="Select a suitable input SAM PART1 file from your history"/>
20 <param name="input_sam_row_part2_file" type="data" format="sam" label="Select a suitable input SAM PART2 file from your history"/>
21 <param name="input_sam_row_part3_file" type="data" format="sam" label="Select a suitable input SAM PART3 file from your history"/>
22 <param name="input_sam_row_part4_file" type="data" format="sam" label="Select a suitable input SAM PART4 file from your history"/>
23 <param name="input_sam_filtered_part1_file" type="data" format="sam" label="Select a suitable input SAM PART1 FILTERED file from your history"/>
24 <param name="input_sam_filtered_part2_file" type="data" format="sam" label="Select a suitable input SAM PART2 FILTERED file from your history"/>
25 <param name="input_sam_filtered_part3_file" type="data" format="sam" label="Select a suitable input SAM PART3 FILTERED file from your history"/>
26 <param name="input_sam_filtered_part4_file" type="data" format="sam" label="Select a suitable input SAM PART4 FILTERED file from your history"/>
27
28
29 <param name="input_mpileup_variant_file" type="data" format="pileup" label="Select a suitable input MPILEUP VARIANT file from your history"/>
30 <param name="input_list_filtered_file" type="data" format="pileup" label="Select a suitable input LIST FILTERED file from your history"/>
31
32 <param name="input_blast_filtered_part1_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART1 file from your history"/>
33 <param name="input_blast_filtered_part2_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART2 file from your history"/>
34 <param name="input_blast_filtered_part3_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART3 file from your history"/>
35 <param name="input_blast_filtered_part4_file" type="data" format="pileup" label="Select a suitable input BLAST FILTERED PART4 file from your history"/>
36
37 <param name="input_snp_selected_file" type="data" format="pileup" label="Select a suitable input SNP SELECTED file from your history"/>
38 </inputs>
39 <outputs>
40 <data name="output_file" format="txt" label="STATS"/>
41 </outputs>
42
43
44 <help>
45
46 </help>
47 </tool>