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