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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 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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4 <!--
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5 Note:
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6 fasta_formatter also has a tabular output mode (-t),
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7 but Galaxy already contains such a tool, so no need
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8 to offer the user a duplicated tool.
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9
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10 So this XML tool only changes the width (line-wrapping) of a
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11 FASTA file.
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12 -->
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13 <command>zcat -f '$input' | fasta_formatter -w $width -o $output</command>
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14 <inputs>
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15 <param format="fasta" name="input" type="data" label="Library to re-format" />
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16
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17 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
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18 </inputs>
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19
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20 <tests>
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21 <test>
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22 <!-- Re-format a FASTA file into a single line -->
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23 <param name="input" value="fasta_formatter1.fasta" />
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24 <param name="width" value="0" />
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25 <output name="output" file="fasta_formatter1.out" />
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26 </test>
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27 <test>
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28 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
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29 <param name="input" value="fasta_formatter1.fasta" />
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30 <param name="width" value="60" />
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31 <output name="output" file="fasta_formatter2.out" />
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32 </test>
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33 </tests>
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34
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35 <outputs>
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36 <data format="input" name="output" metadata_source="input" />
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37 </outputs>
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38
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39 <help>
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40 **What it does**
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41
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42 This tool re-formats a FASTA file, changing the width of the nucleotides lines.
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43
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44 **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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45
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46 --------
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47
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48 **Example**
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49
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50 Input FASTA file (each nucleotides line is 50 characters long)::
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51
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52 >Scaffold3648
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53 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
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54 CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
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55 TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
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56 ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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57 >Scaffold9299
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58 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
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59 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
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60 aactggtctttacctTTAAGTTG
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61
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62
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63 Output FASTA file (with width=80)::
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64
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65 >Scaffold3648
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66 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
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67 ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
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68 ATTTTAATGAACATGTAGTAAAAACT
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69 >Scaffold9299
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70 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
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71 GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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72
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73 Output FASTA file (with width=0 => single line)::
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74
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75 >Scaffold3648
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76 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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77 >Scaffold9299
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78 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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79 </help>
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80 </tool>
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