Mercurial > repos > swebb > pycrac

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author swebb
date Tue, 18 Jun 2013 09:11:00 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:19b20927172d
1 <tool id ="pyBarcodeFilter" name="pyBarcodeFilter" force_history_refresh="True">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="perl">
6 /usr/local/bin/pyBarcodeFilter.pl
7 --file_type $ftype.type
8 -f $ftype.f
9 -b $barcode
10 -m $mismatch
11 $index
12 --out $out
13 --id $out.id
14 --output_path $__new_file_path__
15 #if $ftype.reverse.rev == "yes":
16 -r=$ftype.reverse.r
17 $ftype.reverse.both
18 #end if#
19 </command>
20 <version_command>pyBarcodeFilter.py --version</version_command>
21 <inputs>
22 <conditional name="ftype">
23 <param name="type" type="select" label="File type">
24 <option value="fastq" selected="true">FASTQ</option>
25 <option value="fasta">FASTA</option>
26 </param>
27 <when value="fastq">
28 <param format="fastq" name="f" type="data" label="FastQ File -f" help="FastQ format" />
29 <conditional name="reverse">
30 <param name="rev" type="select" label="Add a reverse or paired FastQ file">
31 <option value="no" selected="true">NO</option>
32 <option value="yes">YES</option>
33 </param>
34 <when value="yes">
35 <param format="fastq" name="r" type="data" label="Reverse FastQ File -f" help="FastQ format" />
36 <param name="both" type="select" label="Search for barcode in both reads">
37 <option value="" selected="true">NO</option>
38 <option value="--both">YES</option>
39 </param>
40 </when>
41 <when value="no">
42 </when>
43 </conditional>
44 </when>
45 <when value="fasta">
46 <param format="fasta" name="f" type="data" label="FastA File -f" help="FastA format" />
47 <conditional name="reverse">
48 <param name="rev" type="select" label="Add a reverse or paired FastA file">
49 <option value="no" selected="true">NO</option>
50 <option value="yes">YES</option>
51 </param>
52 <when value="yes">
53 <param format="fasta" name="r" type="data" label="Reverse FastA File -f" help="FastA format" />
54 <param name="both" type="select" label="Search for barcode in both reads">
55 <option value="" selected="true">NO</option>
56 <option value="--both">YES</option>
57 </param>
58 </when>
59 <when value="no">
60 </when>
61 </conditional>
62 </when>
63 </conditional>
64 <param format="tabular" name="barcode" type="data" label="Barcode File -f" help="Tab delimited file with barcodes and barcode names" />
65 <param format="integer" name="mismatch" type="integer" label="Mismatches -m" value="0" size="3" help="Set the number of allowed mismatches in a barcode">
66 <validator type="in_range" min="0" max="100" message="Please enter a value between 0 and 100"/>
67 </param>
68 <param name="index" type="select" label="Split data using Illumina indexing barcode information -i">
69 <option value="" selected="true">NO</option>
70 <option value="-i">YES</option>
71 </param>
72 </inputs>
73 <outputs>
74 <data format="text" name="out" label="pyBarcodeFilter"/>
75 </outputs>
76 <help>
77
78 .. class:: infomark
79
80 **pySolexaBarcodeFilter**
81
82 pySolexaBarcodeFilter is part of the pyCRAC_ package. Filters sequence files by barcodes.
83
84 This tool requires FASTA or FASTQ input files containing the raw data and a text file containing barcode information.
85 To process paired end data, use -f and the -r flags to indicate the path to the forward and reverse sequencing reactions, respectively.
86 The barcodes file should two columns separated by a tab (see the table below). The first column should contain the barcode nucleotide sequences.
87 The second column should contain an identifier, for example, the name of the barcode or the name of the experiment.
88 The ’N’ in the barcode sequence indicates a random nucleotide. Make sure to use a simple text editor like TextEdit (MacOS X), gedit (Linux/Unix) or use a text editor in the terminal.
89 The program is case sensitive: all the nucleotide sequences should be upper case.
90 You can freely combine different barcodes but if you are mixing samples containing random nucleotide barcodes and normal barcodes.
91 **NOTE!** make sure to place the regular barcode sequence below the sequence with random nucleotides and make sure the shortest sequence is ALWAYS at the bottom in the column (see below)
92
93 Example of a barcode text file::
94
95 NNNCGCTTAGC mutant2
96 NNNGCGCAGC mutant1
97 NNNATTAG control
98 NNNTAAGC myfavprotein
99 AGC oldcontrol
100 AC veryfirstbarcodedsample
101
102 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
103
104 ------
105
106 **Parameter list**
107
108 Options::
109
110 -f FILE, --input_file=FILE
111 name of the FASTQ or FASTA input file
112 -r FILE, --reverse_input_file=FILE
113 name of the paired (or reverse) FASTQ or FASTA input file
114 --file_type=FASTQ
115 type of file, uncompressed (fasta or fastq) or compressed (fasta.gz or fastq.gz, gzip/gunzip
116 compressed). Default is fastq
117 -b FILE, --barcode_list=FILE
118 name of tab-delimited file containing barcodes and barcode names
119 -m 1, --mismatches=1
120 to set the number of allowed mismatches in a barcode. A maximum of one mismatch is allowed. Default = 0
121 -i, --index
122 use this option if you want to split the data using the Illumina indexing barcode information
123
124 </help>
125 </tool>