Mercurial > repos > jgarbe > redup
comparison redup.xml @ 0:df1e7c7dd9cb draft default tip
Initial uploaded of files
| author | jgarbe |
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| date | Wed, 27 Nov 2013 14:39:56 -0500 |
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| -1:000000000000 | 0:df1e7c7dd9cb |
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| 1 <tool id="redup" name="Redup" version="1.0"> | |
| 2 <description>Remove exact duplicate reads from paired-end fastq files</description> | |
| 3 <command interpreter="perl"> | |
| 4 ## Need to handle file names, probably should fix redup.pl | |
| 5 redup.pl | |
| 6 #if $opt_n: | |
| 7 -n $opt_n | |
| 8 #end if | |
| 9 $fastq1_in $fastq2_in $unique1_out $unique2_out | |
| 10 #if $opt_n: | |
| 11 > $duplicates | |
| 12 #end if | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param name="fastq1_in" type="data" format="fastq" label="Fastq Input 1"/> | |
| 16 <param name="fastq2_in" type="data" format="fastq" label="Fastq Input 2"/> | |
| 17 <param name="opt_n" type="integer" value="20" optional="true" label="Number of most duplicated sequences printed out. (default 20)"> | |
| 18 <validator type="in_range" message="Value can not be negative" min="0"/> | |
| 19 </param> | |
| 20 </inputs> | |
| 21 <stdio> | |
| 22 <exit_code range="1:" level="fatal"/> | |
| 23 </stdio> | |
| 24 <outputs> | |
| 25 <data format_source="fastq1_in" name="unique1_out" label="${tool.name} on ${on_string}: fastq1.unique" /> | |
| 26 <data format_source="fastq2_in" name="unique2_out" label="${tool.name} on ${on_string}: fastq2.unique" /> | |
| 27 <data format="fasta" name="duplicates" label="${tool.name} on ${on_string}: top duplicates" > | |
| 28 <filter>opt_n != None</filter> | |
| 29 </data> | |
| 30 </outputs> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="fastq1_in" ftype="fastq" value="input1.fastq" /> | |
| 34 <param name="fastq2_in" ftype="fastq" value="input2.fastq" /> | |
| 35 <param name="opt_n" value="20" /> | |
| 36 <output name="unique1_out" file="output1.fastq" /> | |
| 37 <output name="unique2_out" file="output2.fastq" /> | |
| 38 <output name="duplicates" file="duplicates.fasta" /> | |
| 39 </test> | |
| 40 </tests> | |
| 41 | |
| 42 <help> | |
| 43 This script removes duplicate paired-end reads from the input files sample1_R1.fastq and sample1_R2.fastq and prints out unique reads to the files sample1_R1.fastq.unique and sample2_R2.fastq.unique. Reads must have the exact same sequence to be called duplicates, quality scores are ignored. The top N (default 20) most duplicated sequences are printed out in fasta format, making it convenient for using BLAST to identify them. | |
| 44 </help> | |
| 45 </tool> |