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1 <!--
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2 # =====================================================
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3 # $Id: FastaStats.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $
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4 # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/FastaStats.xml $
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5 # $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $
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6 # $LastChangedRevision: 90 $
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7 # $LastChangedBy: pieter.neerincx@gmail.com $
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8 # =====================================================
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9 -->
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10 <tool id="FastaStats1" name="FastaStats">
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11 <description>List statistics for sequences in a FASTA file</description>
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12 <command interpreter="perl">FastaStats.pl $get_positional_composition_stats -i $input -o $output -l WARN</command>
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13 <inputs>
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14 <param format="fasta" name="input" type="data" label="FASTA sequences"/>
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15 <param name="get_positional_composition_stats" type="boolean" truevalue="-p" falsevalue="" optional="true" label="Calculate positional acid frequencies"/>
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16 </inputs>
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17 <outputs>
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18 <data format="txt" name="output" label="FASTA Statistics for ${input.name}"/>
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input" value="fasta_2_proteins.fasta" ftype="fasta"/>
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23 <output name="output" file="FastaStats_example_output.txt"/>
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24 </test>
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25 </tests>
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26 <help>
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27
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28 .. class:: infomark
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29
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30 **What it does**
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31
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32 This tool analyzes a collection of sequences in FASTA format and reports: \
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33
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34 - The total number of sequences.
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35 - The total number of nucleotide or amino acids.
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36 - The total frequency of nucleotide or amino acids.
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37 - The positional frequency of nucleotide or amino acids (optional).
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38
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39 -----
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40
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41 **Example**
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42
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43 If the FASTA sequence collection contains these two sequences::
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44
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45 >UniProtKB:Q42593 L-ascorbate peroxidase T, chloroplastic;
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46 MSVSLSAASHLLCSSTRVSLSPAVTSSSSSPVVALSSSTSPHSLGSVASSSLFPHSSFVL
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47 QKKHPINGTSTRMISPKCAASDAAQLISAKEDIKVLLRTKFCHPILVRLGWHDAGTYNKN
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48 IEEWPLRGGANGSLRFEAELKHAANAGLLNALKLIQPLKDKYPNISYADLFQLASATAIE
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49 EAGGPDIPMKYGRVDVVAPEQCPEEGRLPDAGPPSPADHLRDVFYRMGLDDKEIVALSGA
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50 HTLGRARPDRSGWGKPETKYTKTGPGEAGGQSWTVKWLKFDNSYFKDIKEKRDDDLLVLP
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51 TDAALFEDPSFKNYAEKYAEDVAAFFKDYAEAHAKLSNLGAKFDPPEGIVIENVPEKFVA
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52 AKYSTGKKELSDSMKKKIRAEYEAIGGSPDKPLPTNYFLNIIIAIGVLVLLSTLFGGNNN
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53 SDFSGF
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54 >UniProtKB:A0MQ79 Ascorbate peroxidase;
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55 MVKNYPVVSEEYLIAVDKAKKKLRGFIAEKNCAPLMLRLAWHSAGTFDQCSRTGGPFGTM
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56 RFKAEQAHSANNGIDIAIRLLEPIKEQFPILSYADFYQLAGVVAVEVTGGPEVPFHPGRP
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57 DKEEPPVEGRLPDAYKGSDHLRDVFIKQMGLSDQDIVALSGGHTLGRCHKERSGFEGPWT
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58 ENPLIFDNSYFKELVCGERDGLLQLPSDKALLADPVFHPLVEKYAADEDAFFADYAEAHL
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59 KLSELGFADA
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60
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61 The reported stats (without optional positional acid frequencies) will be this::
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62
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63 Sequences 2
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64 Acid A 69
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65 Acid C 8
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66 Acid D 44
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67 Acid E 44
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68 Acid F 33
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69 Acid G 52
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70 Acid H 18
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71 Acid I 30
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72 Acid K 50
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73 Acid L 67
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74 Acid M 9
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75 Acid N 22
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76 Acid P 46
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77 Acid Q 13
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78 Acid R 26
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79 Acid S 57
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80 Acid T 23
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81 Acid V 37
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82 Acid W 7
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83 Acid Y 21
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84 Total acids 676
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85
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86 </help>
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87 </tool>
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