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annotate fasta_formatter.xml @ 2:61469a8970cd draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:39:03 -0400
parents 2cbdd2fc365b
children 4f66158f20f2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1 <tool id="cshl_fasta_formatter" version="1.0.0" name="FASTA Width">
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2 <description>formatter</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
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5 </requirements>
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6 <!--
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7 Note:
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8 fasta_formatter also has a tabular output mode (-t),
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9 but Galaxy already contains such a tool, so no need
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10 to offer the user a duplicated tool.
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11
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12 So this XML tool only changes the width (line-wrapping) of a
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13 FASTA file.
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14 -->
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15 <command>
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16 <![CDATA[
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17 zcat -f < '$input' | fasta_formatter -w $width -o '$output'
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param format="fasta" name="input" type="data" label="Library to re-format" />
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22
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23 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
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24 </inputs>
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25 <outputs>
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26 <data format="fasta" name="output" metadata_source="input" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <!-- Re-format a FASTA file into a single line -->
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31 <param name="input" value="fasta_formatter1.fasta" />
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32 <param name="width" value="0" />
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33 <output name="output" file="fasta_formatter1.out" />
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34 </test>
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35 <test>
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36 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
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37 <param name="input" value="fasta_formatter1.fasta" />
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38 <param name="width" value="60" />
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39 <output name="output" file="fasta_formatter2.out" />
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40 </test>
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41 </tests>
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42 <help>
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43 **What it does**
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44
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45 This tool re-formats a FASTA file, changing the width of the nucleotides lines.
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46
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47 **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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48
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49 --------
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50
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51 **Example**
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52
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53 Input FASTA file (each nucleotides line is 50 characters long)::
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54
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55 >Scaffold3648
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56 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
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57 CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
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58 TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
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59 ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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60 >Scaffold9299
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61 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
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62 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
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63 aactggtctttacctTTAAGTTG
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64
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65
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66 Output FASTA file (with width=80)::
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67
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68 >Scaffold3648
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69 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
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70 ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
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71 ATTTTAATGAACATGTAGTAAAAACT
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72 >Scaffold9299
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73 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
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74 GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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75
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76 Output FASTA file (with width=0 => single line)::
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77
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78 >Scaffold3648
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79 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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80 >Scaffold9299
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81 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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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>