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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author vipints
date Tue, 07 Jun 2011 17:29:24 -0400
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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1 <tool id="gff_available_limits" name="FeatureScan" version="1.0.0">
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2 <description>gives an overview about GFF file content</description>
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3 <command interpreter="python">
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4 gff_available_limits.py
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5 $gff_input
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6 > $overview
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7 </command>
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8 <inputs>
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9 <param format="gff3" name="gff_input" type="data" label="Genome annotation in GFF3 format" help="Genome annotation in GFF3 format describing the known gene structures and other features for the provided genome."/>
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10 </inputs>
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11 <outputs>
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12 <data format="txt" name="overview" label="Feature contents in GFF file" />
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13 </outputs>
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14 <tests>
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15 <test>
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16 <param name="gff_input" value="GFF_2_Source.gff3" />
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17 <output name="overview" file="GFF_2_Source_FeatureScan.txt" />
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18 </test>
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19 </tests>
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20 <help>
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21
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22 **What it does**
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23
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24 This tool provides an overview of available contig identifiers, sources and feature types and their corresponding counts from a given GFF file.
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25
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26 --------
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27
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28 **Example**
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29
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30 - The features ID mapping in the following data in GFF format::
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31
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32 ##gff-version 3
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33 scaffold_1 JGI_Filtered gene 33131338 33131726 . - . ID=scaffold_105720.1;Name=scaffold_105720.1
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34 scaffold_1 JGI_Filtered mRNA 33131338 33131726 . - . ID=Transcript:924439;Name=Transcript:924439;Parent=scaffold_105720.1
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35 scaffold_1 JGI_Filtered three_prime_UTR 33131338 33131357 . - . ID=three_prime_UTR:924439;Parent=Transcript:924439
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36 scaffold_1 JGI_Filtered exon 33131338 33131654 . - . ID=exon:924439;Parent=Transcript:924439
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37 scaffold_1 JGI_Filtered CDS 33131358 33131654 . - 0 ID=CDS:924439;Parent=Transcript:924439;Name=scaffold_105720.1
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38 scaffold_1 JGI_Filtered exon 33131703 33131726 . - . ID=exon:924439;Parent=Transcript:924439
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39 scaffold_1 JGI_Filtered CDS 33131703 33131705 . - 0 ID=CDS:924439;Parent=Transcript:924439;Name=scaffold_105720.1
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40 scaffold_1 JGI_Filtered five_prime_UTR 33131706 33131726 . - . ID=five_prime_UTR:924439;Parent=Transcript:924439
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41 Chr4 TAIR9 gene 1180 1536 . - . ID=AT4G00005;Note=protein_coding_gene;Name=AT4G00005
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42 Chr4 TAIR9 mRNA 1180 1536 . - . ID=AT4G00005.1;Parent=AT4G00005;Name=AT4G00005.1;Index=1
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43 Chr4 TAIR9 protein 1180 1536 . - . ID=AT4G00005.1-Protein;Name=AT4G00005.1;Derives_from=AT4G00005.1
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44 Chr4 TAIR9 CDS 1180 1536 . - 0 Parent=AT4G00005.1,AT4G00005.1-Protein;
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45 Chr4 TAIR9 exon 1180 1536 . - . Parent=AT4G00005.1
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46
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47 - Will be displayed as::
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48
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49 Chromosome identifier(s) and corresponding count:
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50 Chr4 5
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51 scaffold_1 8
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52
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53 Source(s) of feature and corresponding count:
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54 JGI_Filtered 8
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55 TAIR9 5
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56
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57 Feature type(s) and corresponding count:
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58 gene 2
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59 mRNA 2
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60 five_prime_UTR 1
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61 three_prime_UTR 1
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62 exon 3
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63 CDS 3
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64 protein 1
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65
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66 Unique combination of Feature type(s), Source(s) and corresponding count:
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67 JGI_Filtered, CDS 2
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68 JGI_Filtered, exon 2
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69 JGI_Filtered, five_prime_UTR 1
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70 JGI_Filtered, gene 1
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71 JGI_Filtered, mRNA 1
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72 JGI_Filtered, three_prime_UTR 1
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73 TAIR9, CDS 1
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74 TAIR9, exon 1
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75 TAIR9, protein 1
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76 TAIR9, mRNA 1
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77 TAIR9, gene 1
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78
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79 --------
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80
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81 **About formats**
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82
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83 **GFF3 format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields:
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84
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85 1. seqid - Must be a chromosome or scaffold.
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86 2. source - The program that generated this feature.
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87 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
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88 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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89 5. stop - The ending position of the feature (inclusive).
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90 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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91 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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92 8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
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93 9. attributes - All lines with the same group are linked together into a single item.
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94
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95 --------
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96
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97 This tool is a part of the **MLB Group at Friedrich Miescher Laboratory of the Max Planck Society**. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de)
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98 </help>
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99 </tool>