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author galaxyp
date Thu, 14 Sep 2017 16:14:56 -0400
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1 <tool id="validate_fasta_database" name="Validate FASTA Database" version="0.1.4">
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2 <requirements>
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3 <requirement type="package" version="1.0">validate-fasta-database</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1" level="fatal" description="Invalid FASTA headers detected, was asked to fail"/>
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7 </stdio>
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8 <command detect_errors="exit_code"><![CDATA[
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9 validate-fasta-database
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10 '$inFasta'
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11 '$goodFastaOut'
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12 '$badFastaOut'
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13 '$crashIfInvalid'
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14 '$checkIsProtein'
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15 '$customLetters'
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16 '$checkHasAccession'
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17 '$minimumLength'
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18 ]]></command>
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19 <inputs>
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20 <param type="data" name="inFasta" format="fasta" label="Select input FASTA dataset"/>
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21 <param type="boolean" name="crashIfInvalid"
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22 label="Fail job if invalid FASTA headers detected?"
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23 value="false"/>
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24 <param type="boolean" name="checkIsProtein"
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25 label="Ensure that sequence is a valid amino acid sequence?"
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26 help="Checks that sequence only contains the 20 essential amino
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27 acids (and optional non-standard AAs), and checks that is not DNA or RNA"
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28 value="true"/>
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29 <param type="text" name="customLetters" value=""
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30 label="Optional: add one letter codes for any non-standard amino acids that you are using. "
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31 help="Anything that is not an upper case letter [A-Z] will be ignored."/>
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32 <param type="boolean" name="checkHasAccession"
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33 label="Only pass sequences with accession numbers?"
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34 value="false"/>
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35 <param type="integer" name="minimumLength"
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36 label="Minimum length for sequences to pass"
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37 value="0"/>
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38 </inputs>
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39 <outputs>
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40 <data name="goodFastaOut" format="fasta" label="Validate FASTA ${on_string}: passed"/>
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41 <data name="badFastaOut" format="fasta" label="Validate FASTA ${on_string}: failed"/>
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42 </outputs>
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43 <tests>
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44 <!-- test general filtering -->
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45 <test>
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46 <param name="inFasta" value="fastaFilteringTest_IN.fasta"/>
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47 <output name="goodFastaOut" file="fastaFilteringTest_OUT1.fasta" />
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48 <output name="badFastaOut" file="fastaFilteringTest_OUT2.fasta" />
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49 </test>
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50
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51 <!--test filtering out genetic sequences and bad protein sequences-->
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52 <test>
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53 <param name="inFasta" value="geneticFiltering.in"/>
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54 <param name="checkIsProtein" value="true"/>
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55 <output name="goodFastaOut" file="geneticFilteringGood.out"/>
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56 <output name="badFastaOut" file="geneticFilteringBad.out"/>
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57 </test>
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58
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59 <test>
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60 <param name="inFasta" value="length5Filtering.in"/>
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61 <param name="minimumLength" value="5"/>
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62 <output name="goodFastaOut" file="length5FilteringGood.out"/>
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63 <output name="badFastaOut" file="length5FilteringBad.out"/>
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64 </test>
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65 </tests>
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66 <help>
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67
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68 <![CDATA[
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69 **Notes**
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70
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71 Takes a FASTA database and validates the headers using the Compomics (developers of SearchGUI and PeptideShaker) schema.
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72 Custom FASTA databases may be in an invalid format, which causes SearchGUI to crash.
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73
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74 **Output**
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75
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76 The main output of this tool, "Validate FASTA: Passed Sequences", is a FASTA database that can be run through SearchGUI without error.
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77 The failed sequences may be examined for typos and other errors.
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78
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79 In addition, the tool will print the databases assigned by the Compomics utility (i.e., UniProt), for a quick check of the validity of the custom FASTA database.
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80
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81 Sequences that may cause the tool to report an exception are those that are not valid examples of the following formats:
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82 * UniProt,
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83 * SwissProt (starts with ">sw|" or ">SW|")
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84 * NCBI (starts with ">gi|" or ">GI|")
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85 * Halobacterium from Max Planck (starts with "OE")
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86 * H Influenza, from Novartis (starts with ">hflu_")
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87 * C Trachomatis (starts with ">C.tr\_" or "C\_trachomatis\_")
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88 * M Tuberculosis (starts with ">M. tub")
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89 * Saccharomyces Genome Database (contains "SGDID")
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90 * Genome translation (ex. ">dm345\_3L-sense [2343534-234353938]")
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91 * Genome Annotation Framework for Flexible Analysis (GAFFA) (starts with ">GAFFA")
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92 * UPS (contains "\_HUMAN\_UPS")
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93
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94 Many sequences are reported as Generic, which may or may not allow for extraction of the accession number.
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95 ]]>
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96 </help>
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97 <citations>
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98 <citation type="bibtex">
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99 @misc{fastaValidationTool,
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100 author = {The GalaxyP Team},
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101 date = {22 June 2017},
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102 title = {FASTA Database Validation Tool}
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103 }
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104 </citation>
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105 </citations>
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106 </tool>