|
0
|
1 <tool id="pyAlignment2Tab" name="pyAlignment2Tab">
|
|
|
2 <description>converter</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package">pyCRAC</requirement>
|
|
|
5 </requirements>
|
|
|
6 <command interpreter="python">/usr/local/bin/pyAlignment2Tab.py -f $input --limit $limit -o $output --singlefile
|
|
|
7 </command>
|
|
|
8 <version_command>/usr/local/bin/pyAlignment2Tab.py --version</version_command>
|
|
|
9 <inputs>
|
|
|
10 <param name="input" type="data" format="fasta" label="pyReadAligner output file -f" help="Fasta file"/>
|
|
|
11 <param name="limit" type="integer" format="integer" value="90" size="4" label="Set the column width of alignment" help="Enter a value > 50">
|
|
|
12 <validator type="in_range" min="50" message="Please enter a value greater than 50"/>
|
|
|
13 </param>
|
|
|
14 <param name="label" type="text" format="txt" size="30" value="pyAlignment2Tab" label="Enter output file label -o" />
|
|
|
15 </inputs>
|
|
|
16 <outputs>
|
|
|
17 <data name="output" format="txt" label="${label.value}.tab"/>
|
|
|
18 </outputs>
|
|
|
19 <help>
|
|
|
20
|
|
|
21 .. class:: infomark
|
|
|
22
|
|
|
23 **pyAlignment2Tab**
|
|
|
24
|
|
|
25 pyAlignment2Tab is part of the pyCRAC_ package. Converts pyReadAligner fasta output to a tabular alignment output.
|
|
|
26
|
|
|
27 Example::
|
|
|
28
|
|
|
29 The tool expects a standard pyReadAligner fasta-formatted output file:
|
|
|
30
|
|
|
31 >GeneX
|
|
|
32 ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAACAGCAGCAGCGAGAGTAGTAGTAACAAAAACAATATCAATGTCGGCGTCGGTGACGATAGCGGTAA
|
|
|
33 >257930-10
|
|
|
34 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT----------------------------------------------------------------------------------------------------------------
|
|
|
35 >3664964-1
|
|
|
36 ---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT----------------------------------------------------------------------------------------------------------------
|
|
|
37 >4033560-1
|
|
|
38 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT----------------------------------------------------------------------------------------------------------------
|
|
|
39 >8571880-1
|
|
|
40 ---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT----------------------------------------------------------------------------------------------------------------
|
|
|
41 >9617396-1
|
|
|
42 ---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT----------------------------------------------------------------------------------------------------------------
|
|
|
43 >843368-5
|
|
|
44 ------------AACAcGGATACAAGACACGCACATTCTG-------------------------------------------------------------------------------------------------------------------
|
|
|
45 >854553-5
|
|
|
46 ------------AACATGGATACAAGACACGCAC--TCTG-------------------------------------------------------------------------------------------------------------------
|
|
|
47 >1522401-2
|
|
|
48 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA-----------------------------------------------------------------------------------------------------
|
|
|
49 >5981234-1
|
|
|
50 --------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA-----------------------------------------------------------------------------------------------------
|
|
|
51 >997684-4
|
|
|
52 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA-----------------------------------------------------------------------------------------------------
|
|
|
53 >1046653-4
|
|
|
54 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC----------------------------------------------------------------------------------------------------
|
|
|
55 >1103730-4
|
|
|
56 ---------------ATGGATACAAGACACGCACAcTCTG-------------------------------------------------------------------------------------------------------------------
|
|
|
57 >1603913-2
|
|
|
58 ---------------ATGGATACAAGAaACGCACAcTCTG-------------------------------------------------------------------------------------------------------------------
|
|
|
59 >180349-12
|
|
|
60 ---------------ATGGATACAAGACACGCACATTCcGCTTTACTG-----------------------------------------------------------------------------------------------------------
|
|
|
61 >1985106-1
|
|
|
62 ---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC----------------------------------------------------------------------------------------------------
|
|
|
63 >1987775-1
|
|
|
64 ---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC----------------------------------------------------------------------------------------------------
|
|
|
65 >2258725-1
|
|
|
66 ---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC----------------------------------------------------------------------------------------------------
|
|
|
67 >2631987-1
|
|
|
68 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC----------------------------------------------------------------------------------------------------
|
|
|
69
|
|
|
70 This will be converted into:
|
|
|
71
|
|
|
72 1 .........|.........|.........|.........|.........|.........|.........|.........|.........| 90
|
|
|
73 >GeneX ATGTCTCGTACTAACATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACAGAGTGCTACTGCAAATAGCAGGAGCAGCAAC
|
|
|
74 >257930-10 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGCTT-----------------------------------------------
|
|
|
75 >3664964-1 ---TCTCGcACcAACATGGATACAAGACACGCACATTtTGCTT-----------------------------------------------
|
|
|
76 >4033560-1 ---TCTCGTACcAACATGGATACAAGACACGCACATTCTGtTT-----------------------------------------------
|
|
|
77 >8571880-1 ---TCTCGTACcAACATGGATACAAGACACGCAgATTCTGCTT-----------------------------------------------
|
|
|
78 >9617396-1 ---TCTCGTACcAACATGGATACAAGACACGCcCATTCTGCTT-----------------------------------------------
|
|
|
79 >843368-5 ------------AACAcGGATACAAGACACGCACATTCTG--------------------------------------------------
|
|
|
80 >854553-5 ------------AACATGGATACAAGACACGCAC--TCTG--------------------------------------------------
|
|
|
81 >1522401-2 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgA------------------------------------
|
|
|
82 >5981234-1 --------------CATGGATACAAGACACGCACAcTCTGCTTTACTGGCAGCA------------------------------------
|
|
|
83 >997684-4 --------------CATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCA------------------------------------
|
|
|
84 >1046653-4 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgAC-----------------------------------
|
|
|
85 >1103730-4 ---------------ATGGATACAAGACACGCACAcTCTG--------------------------------------------------
|
|
|
86 >1603913-2 ---------------ATGGATACAAGAaACGCACAcTCTG--------------------------------------------------
|
|
|
87 >180349-12 ---------------ATGGATACAAGACACGCACATTCcGCTTTACTG------------------------------------------
|
|
|
88 >1985106-1 ---------------ATGGATACAAGACACGCACATTCgGCTTTACTGGCAGCcC-----------------------------------
|
|
|
89 >1987775-1 ---------------ATGGATACccGACACGCACATTCTGCTTTACTGcCAGCAC-----------------------------------
|
|
|
90 >2258725-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTgCTGGCAGCAC-----------------------------------
|
|
|
91 >2631987-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGgAC-----------------------------------
|
|
|
92 >337206-9 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCAC-----------------------------------
|
|
|
93 >4616761-1 ---------------ATGGATAgAAGACACGCACATTCTGCTTTACTGGtAGCAC-----------------------------------
|
|
|
94 >4756312-1 ---------------ATGGATACAAcACACGCACAcTCTG--------------------------------------------------
|
|
|
95 >4763682-1 ---------------ATGGATACAAGACACGCACATTCcGCTTTcCTG------------------------------------------
|
|
|
96 >5971268-1 ---------------ATGGATACAAGACACGCACATTCcGCTcTACTc------------------------------------------
|
|
|
97 >6644790-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTcGCAGCAC-----------------------------------
|
|
|
98 >7112423-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGtCAGCAC-----------------------------------
|
|
|
99 >7559990-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCcGgAC-----------------------------------
|
|
|
100 >8007281-1 ---------------ATGGATAtAAGACACGCACAcTCTG--------------------------------------------------
|
|
|
101 >9150255-1 ---------------ATGGATACAcGACACGCACATTCcGCTTTcCTG------------------------------------------
|
|
|
102 >9180814-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGgcC-----------------------------------
|
|
|
103 >963117-4 ---------------ATGGATACAAGACACGCACATTCTGCTTTACcGGCAGCAC-----------------------------------
|
|
|
104 >9672073-1 ---------------ATGGATACAAGACACGCACATTCTGCTTTACTGGCAGCcC-----------------------------------
|
|
|
105 >971218-4 ---------------ATGGATACAAGACACGCACATcCTGCTTTACTGG-AGCACC----------------------------------
|
|
|
106 >10040274-1 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGgACCACA-------------------------------
|
|
|
107 >1063072-4 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCACCACA-------------------------------
|
|
|
108 >1430188-2 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCACA-------------------------------
|
|
|
109 >5196741-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCcGCACCACA-------------------------------
|
|
|
110 >6017337-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGtCAGaACCcCA-------------------------------
|
|
|
111 >7159053-1 -------------------ATACAAGACACGCACATTCTGCTTTACTGGCAGCACCcaA-------------------------------
|
|
|
112 >7528336-1 -------------------ATACAAGACACGCACATTCTGCTTcACTGGCAGCAaCACA-------------------------------
|
|
|
113 >735584-6 --------------------------------------------------------ACAGAGTGCTACTGCAAAcAGCAGGAGCAGCAAC
|
|
|
114 >8551047-1 --------------------------------------------------------ACAGAGTGCTAtTGCAAAcAGCAGGAGtAGtAAC
|
|
|
115 >3000121-1 ------------------------------------------------------------AGTcCTACcGCAAATAGCAGcAGCAGCAAC
|
|
|
116 >928481-5 ------------------------------------------------------------AGTGCTACcGCAAATAGCAGGAGCAGCAAC
|
|
|
117 >126987-15 ----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC
|
|
|
118 >3122797-1 ----------------------------------------------------------------------CAAATAGCAGGcGCAGCAAC
|
|
|
119 >6684686-1 ----------------------------------------------------------------------CAAATAGCAGGAGCAGCAAC
|
|
|
120
|
|
|
121 Note that the column width here was set to 90 characters
|
|
|
122
|
|
|
123 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
|
|
|
124
|
|
|
125 ------
|
|
|
126
|
|
|
127 **Parameter list**
|
|
|
128
|
|
|
129 Options::
|
|
|
130
|
|
|
131 -f data.fasta
|
|
|
132 Type the path to the fasta file that you want to use.
|
|
|
133 --limit=90
|
|
|
134 Allows the user to set the column width of the alignment. Default=90 characters
|
|
|
135 -o output.fasta
|
|
|
136 Provide the name of your output file
|
|
|
137
|
|
|
138 </help>
|
|
|
139 </tool>
|
