Mercurial > repos > devteam > fasta_to_tabular

annotate fasta_to_tabular.xml @ 2:ff4751ce764d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
author devteam
date Sun, 01 Mar 2020 12:23:22 +0000
parents 5cabbe4cfaf4
children 5b998d13de71
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2
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1 <tool id="fasta2tab" name="FASTA-to-Tabular" version="1.1.1" profile="16.04">
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2 <description>converter</description>
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3 <requirements>
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4 <requirement type="package" version="3.7">python</requirement>
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5 </requirements>
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6 <command>
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7 python '$__tool_directory__/fasta_to_tabular.py' '$input' '$output' $keep_first $descr_columns
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8 </command>
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9 <inputs>
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10 <param name="input" type="data" format="fasta" label="Convert these sequences"/>
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11 <param name="descr_columns" type="integer" value="1" min="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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12 </param>
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13 <param name="keep_first" type="integer" value="0" min="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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14 </param>
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15 </inputs>
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16 <outputs>
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17 <data name="output" format="tabular"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="input" value="454.fasta" />
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22 <param name="descr_columns" value="1"/>
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23 <param name="keep_first" value="0"/>
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24 <output name="output" file="fasta_to_tabular_out1.tabular" />
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25 </test>
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26
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27 <test>
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28 <param name="input" value="4.fasta" />
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29 <param name="descr_columns" value="1"/>
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30 <param name="keep_first" value="0"/>
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31 <output name="output" file="fasta_to_tabular_out2.tabular" />
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32 </test>
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34 <test>
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35 <param name="input" value="454.fasta" />
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36 <param name="descr_columns" value="1"/>
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37 <param name="keep_first" value="14"/>
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38 <output name="output" file="fasta_to_tabular_out3.tabular" />
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39 </test>
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41 <test>
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42 <param name="input" value="454.fasta" />
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43 <param name="descr_columns" value="2"/>
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44 <param name="keep_first" value="0"/>
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45 <output name="output" file="fasta_to_tabular_out4.tabular" />
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46 </test>
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47
2
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48 <test>
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49 <param name="input" value="454.fasta" />
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50 <param name="descr_columns" value="5"/>
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51 <param name="keep_first" value="0"/>
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52 <output name="output" file="fasta_to_tabular_out5.tabular" />
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53 </test>
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54
2
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55 <test>
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56 <param name="input" value="454.fasta" />
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57 <param name="descr_columns" value="5"/>
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58 <param name="keep_first" value="10"/>
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59 <output name="output" file="fasta_to_tabular_out6.tabular" />
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60 </test>
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61
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62 </tests>
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63 <help><![CDATA[
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64
0
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65 **What it does**
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66
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67 This tool converts FASTA formatted sequences to TAB-delimited format.
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68
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69 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.
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70 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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71 In some cases the description can be usefully broken up into more columns -- see the examples .
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72
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73 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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74 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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75
2
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76 -----
0
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77
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78 **Example**
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79
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80 Suppose you have the following FASTA formatted sequences from a Roche (454) FLX sequencing run::
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81
2
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82 >EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_
0
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83 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGCGCGATGACCATCGCCCGCTCCACCACG
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84 TTCGGCCGGCCCTTCTCGTCGAGGAATGACACCAGCGCTTCGCCCACG
2
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85 >EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_
0
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86 AATAAAACTAAATCAGCAAAGACTGGCAAATACTCACAGGCTTATACAATACAAATGTAA
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87
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88 Running this tool with the default settings will produce this (2 column output):
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89
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90 ========================================================================== =======================================
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91 EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
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92 EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
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93 ========================================================================== =======================================
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94
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95 Having the full title line (the FASTA "&gt;" line text) as a column is not always ideal.
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96
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97 The **How many characters to keep?** option is useful if your identifiers are all the same length.
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98 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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99
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100 ============== =======================================
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101 EYKX4VC02EQLO5 TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
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102 EYKX4VC02D4GS2 AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
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103 ============== =======================================
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104
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105 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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106 Running this tool with **How many columns to divide title string into?** to **2** will produce this (3 column output):
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107
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108 ============== =========================================================== =======================================
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109 EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
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110 EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
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111 ============== =========================================================== =======================================
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112
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113 Running this tool with **How many columns to divide title string into?** to **5** will produce this (5 column output):
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114
ae709fd50581 Imported from capsule None
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115 ============== ========== ============ ======== ========================== =======================================
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116 EYKX4VC02EQLO5 length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
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117 EYKX4VC02D4GS2 length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
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118 ============== ========== ============ ======== ========================== =======================================
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119
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120 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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121 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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122
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123 ========== ========== ============ ======== ========================== =======================================
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124 EYKX4VC02E length=108 xy=1826_0455 region=2 run=R_2007_11_07_16_15_57_ TCCGCGCCGAGCATGCCCATCTTGGATTCCGGC...ACG
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125 EYKX4VC02D length=60 xy=1573_3972 region=2 run=R_2007_11_07_16_15_57_ AATAAAACTAAATCAGCAAAGACTGGCAAATAC...TAA
ae709fd50581 Imported from capsule None
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126 ========== ========== ============ ======== ========================== =======================================
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127
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128 Note the sequences have been truncated for display purposes in the above tables.
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129
2
ff4751ce764d "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/fasta_to_tabular commit cd1ed08574b749eee2a3f6e6151dbb0c8ca15bbf"
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130 ]]></help>
0
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131 </tool>