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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_parent_child_relation" name="Examine" version="1.0.0">
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2 <description>Parent-Child relation in GFF file</description>
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3 <command interpreter="python">
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4 gff_id_mapper.py
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5 $gff_input
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6 > $idmapping
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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="idmapping" label="Parent-child relation 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="Feature_ID_mapping_W.gff3" />
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17 <output name="idmapping" file="Feature_ID_mapping_W.txt" />
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18 </test>
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19 <test>
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20 <param name="gff_input" value="Aly_JGI.gff3" />
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21 <output name="idmapping" file="Feature_ID_mapping_R.txt" />
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22 </test>
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23 </tests>
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24 <help>
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25
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26 **What it does**
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27
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28 This tool provides the features(gene, mRNA, UTR's, exon, CDS etc) relationship based on their identifier mapping in a given GFF file.
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29
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30 --------
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31
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32 **Example**
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33
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34 - The features ID mapping in the following data in GFF format::
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35
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36 ##gff-version 3
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37 17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11
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38 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859
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39 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751
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40 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352
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41 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751
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42 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
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43
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44 - Will be displayed as::
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45
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46 FIRST level feature(s):
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47 ('protein_coding', 'gene')
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48
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49 SECOND level feature(s):
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50 ('protein_coding', 'mRNA')
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51
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52 THIRD level feature(s):
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53 ('protein_coding', 'CDS'), ('protein_coding', 'exon'), ('protein_coding', 'five_prime_UTR'), ('protein_coding', 'three_prime_UTR')
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54
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55 --------
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56
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57 **About formats**
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58
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59 **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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60
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61 1. seqid - Must be a chromosome or scaffold.
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62 2. source - The program that generated this feature.
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63 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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64 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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65 5. stop - The ending position of the feature (inclusive).
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66 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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67 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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68 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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69 9. attributes - All lines with the same group are linked together into a single item.
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70
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71 --------
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72
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73 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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74 </help>
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75 </tool>