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comparison fasta_to_tabular.xml @ 0:ae709fd50581 draft

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Imported from capsule None
author devteam
date Mon, 19 May 2014 11:00:01 -0400
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1 <tool id="fasta2tab" name="FASTA-to-Tabular" version="1.1.0">
2 <description>converter</description>
3 <command interpreter="python">fasta_to_tabular.py $input $output $keep_first $descr_columns</command>
4 <inputs>
5 <param name="input" type="data" format="fasta" label="Convert these sequences"/>
6 <param name="descr_columns" type="integer" size="2" value="1" label="How many columns to divide title string into?" help="Typically 2 to take the ID (first word) and decription (rest) as two columns, or 1 to give a single column">
7 <validator type="in_range" min="1" />
8 </param>
9 <param name="keep_first" type="integer" size="5" value="0" label="How many title characters to keep?" help="Applies only to the first column taken from the title string ('0' = keep the whole thing), useful when your sequence identifiers are all the same length.">
10 <validator type="in_range" min="0" />
11 </param>
12 </inputs>
13 <outputs>
14 <data name="output" format="tabular"/>
15 </outputs>
16 <tests>
17 <test>
18 <param name="input" value="454.fasta" />
19 <param name="descr_columns" value="1"/>
20 <param name="keep_first" value="0"/>
21 <output name="output" file="fasta_to_tabular_out1.tabular" />
22 </test>
23
24 <test>
25 <param name="input" value="4.fasta" />
26 <param name="descr_columns" value="1"/>
27 <param name="keep_first" value="0"/>
28 <output name="output" file="fasta_to_tabular_out2.tabular" />
29 </test>
30
31 <test>
32 <param name="input" value="454.fasta" />
33 <param name="descr_columns" value="1"/>
34 <param name="keep_first" value="14"/>
35 <output name="output" file="fasta_to_tabular_out3.tabular" />
36 </test>
37
38 <test>
39 <param name="input" value="454.fasta" />
40 <param name="descr_columns" value="2"/>
41 <param name="keep_first" value="0"/>
42 <output name="output" file="fasta_to_tabular_out4.tabular" />
43 </test>
44
45 <test>
46 <param name="input" value="454.fasta" />
47 <param name="descr_columns" value="5"/>
48 <param name="keep_first" value="0"/>
49 <output name="output" file="fasta_to_tabular_out5.tabular" />
50 </test>
51
52 <test>
53 <param name="input" value="454.fasta" />
54 <param name="descr_columns" value="5"/>
55 <param name="keep_first" value="10"/>
56 <output name="output" file="fasta_to_tabular_out6.tabular" />
57 </test>
58
59 </tests>
60 <help>
61
62 **What it does**
63
64 This tool converts FASTA formatted sequences to TAB-delimited format.
65
66 Many tools consider the first word of the FASTA "&gt;" title line to be an identifier, and any remaining text to be a free form description.
67 It is therefore useful to split this text into two columns in Galaxy (identifier and any description) by setting **How many columns to divide title string into?** to **2**.
68 In some cases the description can be usefully broken up into more columns -- see the examples .
69
70 The option *How many characters to keep?* allows to select a specified number of letters from the beginning of each FASTA entry.
71 With the introduction of the **How many columns to divide title string into?** option this setting is of limited use, but does still allow you to truncate the identifier.
72
73 -----
74
75 **Example**
76
77 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
78
79 &gt;EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
80 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
81 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
82 &gt;EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
83 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAA
84
85 Running this tool with the default settings will produce this (2 column output):
86
87 ========================================================================== =======================================
88 EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
89 EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
90 ========================================================================== =======================================
91
92 Having the full title line (the FASTA "&gt;" line text) as a column is not always ideal.
93
94 The **How many characters to keep?** option is useful if your identifiers are all the same length.
95 In this example the identifier is 14 characters, so setting **How many characters to keep?** to **14** (and leaving **How many columns to divide title string into?** as the default, **1**) will produce this (2 column output):
96
97 ============== =======================================
98 EYKX4VC02EQLO5 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
99 EYKX4VC02D4GS2 AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
100 ============== =======================================
101
102 If however your FASTA file has identifiers of variable length, it is better to split the text into at least two columns.
103 Running this tool with **How many columns to divide title string into?** to **2** will produce this (3 column output):
104
105 ============== =========================================================== =======================================
106 EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
107 EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
108 ============== =========================================================== =======================================
109
110 Running this tool with **How many columns to divide title string into?** to **5** will produce this (5 column output):
111
112 ============== ========== ============ ======== ========================== =======================================
113 EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
114 EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
115 ============== ========== ============ ======== ========================== =======================================
116
117 Running this tool with **How many columns to divide title string into?** to **5** and **How many characters to keep?** to **10** will produce this (5 column output).
118 Notice that only the first column is truncated to 10 characters -- and be careful not to trim your sequence names too much (generally they should be unique):
119
120 ========== ========== ============ ======== ========================== =======================================
121 EYKX4VC02E length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
122 EYKX4VC02D length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
123 ========== ========== ============ ======== ========================== =======================================
124
125 Note the sequences have been truncated for display purposes in the above tables.
126
127 </help>
128 </tool>