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annotate fasta_formatter.xml @ 3:4f66158f20f2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
author iuc
date Tue, 08 May 2018 12:33:30 -0400
parents 61469a8970cd
children 381e98a18f01
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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4f66158f20f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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1 <tool id="cshl_fasta_formatter" version="1.0.1" name="FASTA Width">
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2 <description>formatter</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
4f66158f20f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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6 <expand macro="requirements" />
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7 <!--
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8 Note:
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9 fasta_formatter also has a tabular output mode (-t),
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10 but Galaxy already contains such a tool, so no need
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11 to offer the user a duplicated tool.
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12
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13 So this XML tool only changes the width (line-wrapping) of a
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14 FASTA file.
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15 -->
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4f66158f20f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
iuc
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16 <command detect_errors="exit_code"><![CDATA[
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17 @CATS@ fasta_formatter
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18 -w $width
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19 -o '$output'
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20 ]]></command>
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21 <inputs>
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22 <expand macro="fasta_input" />
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23
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24 <param name="width" type="integer" value="0" label="New width for nucleotides strings" help="Use 0 for single line out." />
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25 </inputs>
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26 <outputs>
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27 <data name="output" format="fasta" metadata_source="input" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <!-- Re-format a FASTA file into a single line -->
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32 <param name="input" value="fasta_formatter1.fasta" />
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33 <param name="width" value="0" />
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34 <output name="output" file="fasta_formatter1.out" />
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35 </test>
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36 <test>
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37 <!-- Re-format a FASTA file into multiple lines wrapping at 60 charactes -->
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38 <param name="input" value="fasta_formatter1.fasta" />
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39 <param name="width" value="60" />
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40 <output name="output" file="fasta_formatter2.out" />
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41 </test>
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42 </tests>
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4f66158f20f2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fasta_formatter commit bbb2e6b6769b03602a8ab97001f88fbec52080a1
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43 <help><![CDATA[
0
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44 **What it does**
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45
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46 This tool re-formats a FASTA file, changing the width of the nucleotides lines.
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47
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48 **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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49
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50 --------
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51
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52 **Example**
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53
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54 Input FASTA file (each nucleotides line is 50 characters long)::
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55
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56 >Scaffold3648
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57 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTC
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58 CCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTG
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59 TTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACA
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60 ATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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61 >Scaffold9299
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62 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
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63 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
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64 aactggtctttacctTTAAGTTG
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65
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66
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67 Output FASTA file (with width=80)::
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68
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69 >Scaffold3648
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70 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTT
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71 ATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCA
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72 ATTTTAATGAACATGTAGTAAAAACT
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73 >Scaffold9299
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74 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTAC
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75 GTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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76
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77 Output FASTA file (with width=0 => single line)::
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78
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79 >Scaffold3648
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80 AGGAATGATGACTACAATGATCAACTTAACCTATCTATTTAATTTAGTTCCCTAATGTCAGGGACCTACCTGTTTTTGTTATGTTTGGGTTTTGTTGTTGTTGTTTTTTTAATCTGAAGGTATTGTGCATTATATGACCTGTAATACACAATTAAAGTCAATTTTAATGAACATGTAGTAAAAACT
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81 >Scaffold9299
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82 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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83
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84 ------
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85
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86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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87
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88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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89 ]]></help>
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90 <expand macro="citations" />
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91 </tool>