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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/fastx_toolkit/fasta_clipping_histogram commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author devteam
date Wed, 11 Nov 2015 12:36:37 -0500
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1 <tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.0">
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2 <description>chart</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 <command>fasta_clipping_histogram.pl $input $outfile</command>
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8 <inputs>
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9 <param format="fasta" name="input" type="data" label="Library to analyze" />
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10 </inputs>
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11
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12 <outputs>
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13 <data format="png" name="outfile" metadata_source="input" />
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14 </outputs>
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15 <tests>
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16 </tests>
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17 <help>
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18 **What it does**
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19
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20 This tool creates a histogram image of sequence lengths distribution in a given fasta dataset file.
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21
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22 **TIP:** Use this tool after clipping your library (with **FASTX Clipper tool**), to visualize the clipping results.
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23
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24 -----
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25
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26 **Output Examples**
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27
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28 In the following library, most sequences are 24-mers to 27-mers.
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29 This could indicate an abundance of endo-siRNAs (depending of course of what you've tried to sequence in the first place).
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30
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31 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_1.png
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32
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33 In the following library, most sequences are 19,22 or 23-mers.
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34 This could indicate an abundance of miRNAs (depending of course of what you've tried to sequence in the first place).
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35
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36 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_2.png
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37
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38 -----
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39
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40 **Input Formats**
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41
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42 This tool accepts short-reads FASTA files. The reads don't have to be short, but they do have to be on a single line, like so::
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43
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44 >sequence1
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45 AGTAGTAGGTGATGTAGAGAGAGAGAGAGTAG
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46 >sequence2
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47 GTGTGTGTGGGAAGTTGACACAGTA
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48 >sequence3
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49 CCTTGAGATTAACGCTAATCAAGTAAAC
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50
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51 If the sequences span over multiple lines::
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52
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53 >sequence1
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54 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAG
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55 TCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAG
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56 aactggtctttacctTTAAGTTG
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57
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58 Use the **FASTA Width Formatter** tool to re-format the FASTA into a single-lined sequences::
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59
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60 >sequence1
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61 CAGCATCTACATAATATGATCGCTATTAAACTTAAATCTCCTTGACGGAGTCTTCGGTCATAACACAAACCCAGACCTACGTATATGACAAAGCTAATAGaactggtctttacctTTAAGTTG
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62
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63 -----
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64
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65 **Multiplicity counts (a.k.a reads-count)**
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66
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67 If the sequence identifier (the text after the '>') contains a dash and a number, it is treated as a multiplicity count value (i.e. how many times that individual sequence repeated in the original FASTA file, before collapsing).
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68
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69 Example 1 - The following FASTA file *does not* have multiplicity counts::
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70
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71 >seq1
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72 GGATCC
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73 >seq2
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74 GGTCATGGGTTTAAA
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75 >seq3
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76 GGGATATATCCCCACACACACACAC
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77
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78 Each sequence is counts as one, to produce the following chart:
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79
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80 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_3.png
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81
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82 Example 2 - The following FASTA file have multiplicity counts::
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83
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84 >seq1-2
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85 GGATCC
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86 >seq2-10
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87 GGTCATGGGTTTAAA
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88 >seq3-3
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89 GGGATATATCCCCACACACACACAC
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90
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91 The first sequence counts as 2, the second as 10, the third as 3, to produce the following chart:
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92
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93 .. image:: ${static_path}/fastx_icons/fasta_clipping_histogram_4.png
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94
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95 Use the **FASTA Collapser** tool to create FASTA files with multiplicity counts.
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96
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97 ------
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98
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99 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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100
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101 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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102 </help>
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103 </tool>