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comparison pyCRAC/pyFastqJoiner.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 ="pyFastqJoiner" name="pyFastqJoiner">
2 <requirements>
3 <requirement type="package">pyCRAC</requirement>
4 </requirements>
5 <command interpreter="python">
6 /usr/local/bin/pyFastqJoiner.py
7 -f $ftype.f1 $ftype.f2
8 -o $out
9 --file_type=$ftype.type
10 #if $joinc.ch == "-c":
11 -c $joinc.c
12 #end if#
13 </command>
14 <version_command>/usr/local/bin/pyFastqJoiner.py --version</version_command>
15 <inputs>
16 <conditional name="ftype">
17 <param name="type" type="select" label="File type">
18 <option value="fastq" selected="true">FASTQ</option>
19 <option value="fasta">FASTA</option>
20 </param>
21 <when value="fastq">
22 <param format="fastq" name="f1" type="data" label="First FastQ File -f" help="FastQ format" />
23 <param format="fastq" name="f2" type="data" label="Second FastQ File -f" help="FastQ format" />
24 </when>
25 <when value="fasta">
26 <param format="fasta" name="f1" type="data" label="First FastA File -f" help="FastA format" />
27 <param format="fasta" name="f2" type="data" label="Second FastA File -f" help="FastA format" />
28 </when>
29 </conditional>
30 <conditional name="joinc">
31 <param name="ch" type="select" label="Insert a character at join">
32 <option value="" selected="true">NO</option>
33 <option value="-c">YES</option>
34 </param>
35 <when value="-c">
36 <param type="text" name="c" label="Add this character -c" value=":" >
37 <validator type="empty_field" message="enter a character or turn this option off" />
38 </param>
39 </when>
40 <when value="">
41 </when>
42 </conditional>
43 <param name="label" type="text" format="txt" size="30" value="pyFastqJoiner" label="Enter output file label -o" />
44 </inputs>
45 <outputs>
46 <data format="input" name="out" label="${label.value}.${ftype.type}"/>
47 <change_format>
48 <when input="ftype.type" value="fasta" format="fasta" />
49 </change_format>
50 </outputs>
51 <help>
52
53 .. class:: infomark
54
55 **pyFastqJoiner**
56
57 pyFastqJoiner is part of the pyCRAC_ package. Merges paired sequences from two fastq or fasta formatted files.
58
59 Example::
60
61 Forward reaction:
62
63 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG
64 CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT
65 +
66 `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYae
67 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA
68 CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG
69 +
70 ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBB
71 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC
72 CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT
73 +
74 bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_ef
75 @FCC102EACXX:3:1101:1574:2214#ATCACGAT/1##CGTTTT
76 CTAATGACCCACTCGGCACCTTACGAAATCAAAGTCT
77 +
78 cdfgYY`cefhhZef\eaggXaceeghfQaeghWNW\
79
80 Reverse reaction:
81
82 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
83 AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
84 +
85 YJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
86 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
87 AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
88 +
89 YJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
90 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
91 GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
92 +
93 PP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
94
95 Here the ":" character is used to split the two sequences. This character tells pyFastqSplitter where to split the sequences.
96 This character is ignored by pyFastqDuplicateRemover
97
98 Result:
99
100 @FCC102EACXX:3:1101:1343:2181#ATCACGAT/1##CAATAG@FCC102EACXX:3:1101:1343:2181#ATCACGAT/2
101 CAAATTAGAGTGTTCAAAGCAGGCGTATTGCTCGAAT:AGCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAGA
102 +
103 `efhYb][bdQQ`eeaeaYbeY^ceU__IXa[^ZYaeYJaSJ`Z`K`YbSb[[daeJRR[YeWd_I^I^ecgc]OV\bdeaegbXb
104 @FCC102EACXX:3:1101:1424:2248#ATCACGAT/1##CCAGGA@FCC102EACXX:3:1101:1424:2248#ATCACGAT/2
105 CTAACCATAAACTATGCCTACTAGGGATCCAGAGGTG:AAGTCCTTTAAGTTACAGCCTTGCGACCATACTACACCCAGAACCCAAA
106 +
107 ^_adddhJbaehbedd`dIb_^cXaRI^BBBBBBBBBYJJ\`JQY\`KJ`gY[[QRYY[[`H[_ceI^e[PYO^IWOHW^eaefhh
108 @FCC102EACXX:3:1101:1623:2036#ATCACGAN/1##CTCAGC@FCC102EACXX:3:1101:1623:2036#ATCACGAN/2
109 CAAAGTTAGGGGATCGAAGATGATCAGATACCGTCGT:GGCCAATCCTTATTGTGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTC
110 +
111 bghfc^YbgbeadggfdffeaS^ac_X^cegaGZ_efPP\`ccQ`eY[bQQ[d`ghehaghfgdg[`gb^bd[ePbH^c_c\a_eg
112
113 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
114
115 ------
116
117 **Parameter list**
118
119 Options::
120
121 -f fastq_file1 fastq_file2
122 Provide the names of two raw data files separated by a single space.
123 Make sure the first file is the data file of the forward (/1) sequencing reaction.
124
125 --file_type=FASTQ
126 Can join fasta and fastq files. Fastq is default
127
128 -o mergedfastq.fastq, --outfile=mergedfastq.fastq
129 provide the name of the output file. By default it
130 will be printed to the standard output
131
132 -c :
133 This option adds the '|' character between the DNA
134 sequences so that it is much easier to split the data
135 again later on
136
137
138 </help>
139 </tool>