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1 <tool id="cshl_fasta_formatter" name="FASTA Width">
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2 <description>formatter</description>
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3 <!--
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4 Note:
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5 fasta_formatter also has a tabular output mode (-t),
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6 but Galaxy already contains such a tool, so no need
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7 to offer the user a duplicated tool.
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8
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9 So this XML tool only changes the width (line-wrapping) of a
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10 FASTA file.
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11 -->
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12 <command>
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13 cat '$input' |
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14 fasta_formatter -w $width -o '$output'</command>
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15 <inputs>
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16 <param format="fasta" name="input" type="data" label="Library to re-format" />
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17
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18 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line output." />
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19 </inputs>
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20
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21 <tests>
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22 <test>
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23 <!-- Re-format a FASTA file into a single line -->
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24 <param name="input" value="fasta_formatter1.fasta" />
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25 <param name="width" value="0" />
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26 <output name="output" file="fasta_formatter1.out" />
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27 </test>
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28 <test>
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29 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
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30 <param name="input" value="fasta_formatter1.fasta" />
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31 <param name="width" value="60" />
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32 <output name="output" file="fasta_formatter2.out" />
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33 </test>
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34 </tests>
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35
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36 <outputs>
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37 <data format="input" name="output" metadata_source="input"
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38 />
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39 </outputs>
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40
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41 <help>
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42 **What it does**
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43
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44 This tool re-formats a FASTA file, changing the width of the nucleotides lines.
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45
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46 **TIP:** Outputting a single line (with **width = 0**) can be useful for scripting (with **grep**, **awk**, and **perl**). Every odd line is a sequence identifier, and every even line is a nucleotides line.
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47
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48 --------
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49
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50 **Example**
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51
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52 Input FASTA file (each nucleotides line is 50 characters long)::
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53
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54 >Scaffold3648
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55 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
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56 CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
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57 TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
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58 ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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59 >Scaffold9299
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60 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
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61 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
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62 aactggtctttacctTTAAGTTG
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63
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64
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65 Output FASTA file (with width=80)::
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66
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67 >Scaffold3648
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68 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
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69 ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
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70 ATTTTAATGAACATGTAGTAAAAACT
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71 >Scaffold9299
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72 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
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73 GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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74
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75 Output FASTA file (with width=0 => single line)::
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76
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77 >Scaffold3648
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78 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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79 >Scaffold9299
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80 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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81
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82
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83 ------
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84
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85 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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86
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87 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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88 </help>
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89 </tool>
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90 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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