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comparison pyCRAC/pyFastqDuplicateRemover.xml @ 0:19b20927172d draft

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author swebb
date Tue, 18 Jun 2013 09:11:00 -0400
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1 <tool id ="pyFastqDuplicateRemover" name="pyFastqDuplicateRemover">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="perl">
6 pyFastqDuplicateRemover.pl
7 -f $ftype.f
8 #if $ftype.reverse.rev == "yes":
9 -r=$ftype.reverse.r
10 --out2 $out2
11 #end if#
12 -o $out
13 --id $out.id
14 </command>
15 <version_command>pyFastqDuplicateRemover.py --version</version_command>
16 <inputs>
17 <conditional name="ftype">
18 <param name="type" type="select" label="File type">
19 <option value="fastq" selected="true">FASTQ</option>
20 <option value="fasta">FASTA</option>
21 </param>
22 <when value="fastq">
23 <param format="fastq" name="f" type="data" label="FastQ File -f" help="FastQ format" />
24 <conditional name="reverse">
25 <param name="rev" type="select" label="Add a reverse or paired FastQ file">
26 <option value="no" selected="true">NO</option>
27 <option value="yes">YES</option>
28 </param>
29 <when value="yes">
30 <param format="fastq" name="r" type="data" label="Reverse FastQ File -f" help="FastQ format" />
31 </when>
32 <when value="no">
33 </when>
34 </conditional>
35 </when>
36 <when value="fasta">
37 <param format="fasta" name="f" type="data" label="FastA File -f" help="FastA format" />
38 <conditional name="reverse">
39 <param name="rev" type="select" label="Add a reverse or paired FastA file">
40 <option value="no" selected="true">NO</option>
41 <option value="yes">YES</option>
42 </param>
43 <when value="yes">
44 <param format="fasta" name="r" type="data" label="Reverse FastA File -f" help="FastA format" />
45 </when>
46 <when value="no">
47 </when>
48 </conditional>
49 </when>
50 </conditional>
51 <param name="label" type="text" format="txt" size="30" value="pyFastqDuplicateRemover" label="Enter output file label -o" />
52 </inputs>
53 <outputs>
54 <data format="fasta" name="out" label="${label.value}.fasta"/>
55 <data format="fasta" name="out2" label="${label.value}_reverse.fasta">
56 <filter>ftype['reverse']['rev'] == "yes"</filter>
57 </data>
58 </outputs>
59 <help>
60
61 .. class:: infomark
62
63 **pyFastqDuplicateRemover**
64
65 pyFastqDuplicateRemover is part of the pyCRAC_ package. Removes identical sequences from fastq and fasta files and returns a fasta file with collapsed data.
66
67 Can also process paired-end data.
68
69 **Examples**
70
71 Unprocessed fastq data with six random nucleotides at 5' end of the read::
72
73 @FCC102EACXX:3:1101:3231:2110#TGACCAAT/1
74 GCGCCTGCCAATTCCATCGTAATGATTAATAGGGACGGTCGGGGGCATC
75 +
76 bb_ceeeegggggiiiiiifghiihiihiiiiiiiiiifggfhiecccc
77
78 After pyBarcodeFilter::
79
80 @FCC102EACXX:3:1101:3231:2110#TGACCAAT/1##GCGCCT
81 TCCATCGTAATGATTAATAGGGACGGTCGGGGGCATC
82 +
83 giiiiiifghiihiihiiiiiiiiiifggfhiecccc
84
85 This entry is printed to the NNNNNNGCCAAT barcode file.
86
87 After pyFastqDuplicateRemover::
88
89 >1_GCGCCT_5/1
90 TCCATCGTAATGATTAATAGGGACGGTCGGGGGCATC
91
92 The '1' indicates that this is the first unique cDNA in the data
93 GCGCCT is the random barcode sequence
94 the '5' indicates that 5 reads were found with identical read and random barcode sequences
95 the '/1' indicates that the seqeuence originates from the forward sequencing reaction
96
97 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
98
99 ------
100
101 **Parameter list**
102
103 Options::
104
105 -f FILE, --input_file=FILE
106 name of the FASTQ or FASTA input file
107
108 -r FILE, --reverse_input_file=FILE
109 name of the paired (or reverse) FASTQ or FASTA input file
110
111 -o FILE, --output_file=FILE
112 Provide the path and name of the fastq or fasta output file. Default is standard output.
113 For paired-end data just provide a file name without file extension (!)
114 </help>
115 </tool>
116
117