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1 <tool id="DLaGiFer_3" name="Common attributes selection" version="1.0.0">
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2 <description>Extraction of common sequences attributes</description>
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3 <command interpreter="perl">
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4 paso4.pl "$infile" "$outfile"
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5 </command>
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6
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7 <inputs>
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8 <param name="infile" type="data" format="gff" label="Sequence in Fasta File"/>
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9
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10
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11 </inputs>
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12 <outputs><data format="txt" name="outfile"/>
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13 </outputs>
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14
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15 <stdio><exit_code range="1:" level="fatal" description="Error" /></stdio>
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16 <help>
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17
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18
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19 **What it does**
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20
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21 This tool obtains certain common attributes of the sequences contained in a gff3 format file.
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22
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23
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24 **Dependencies**
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25
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26 Perl is required for running this tool.
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27
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28
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29
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30 #####
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31 Input
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32 #####
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33
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34 A gff3 file with protein attributes is required.
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35
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36 Generic Feature Format Version 3 (GFF3)
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37
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38 The GFF3 format is a flat tab-delimited file, which is much richer then the TSV output format. It allows you to trace back from matches to predicted proteins and to nucleic acid sequences. It also contains a FASTA format representation of the predicted protein sequences and their matches. You will find a documentation of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].
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39
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40
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41 ######
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42 Output
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43 ######
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44
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45
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46 A text file is generated by this tool.
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47
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48 Example Output
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49 --------------
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50
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51 The common atributes of the sequences Q0KIY3 P02185 P02178 Q0KIY5 Q0KIY1 are:
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52
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53 For Name atribute: SSF46458 PF00042 PR00613 G3DSA:1.10.490.10 PS01033
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54
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55 For Ontology_term atribute: "GO:0005506" "GO:0020037" "GO:0015671" "GO:0019825"
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56
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57 For Dbxref atribute: "InterPro:IPR009050" "InterPro:IPR000971" "InterPro:IPR002335" "InterPro:IPR012292"
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58
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59
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60
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61 **Galaxy Wrapper Authors**::
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62
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63 * Laura Entrambasaguas
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64 * Ginés Almagro
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65 * Fernando Pérez
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66
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67 </help>
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68 </tool>
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