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1 <tool id ="pyExtractLinesFromGTF" name="pyExtractLinesFromGTF">
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2 <requirements>
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3 <requirement type="package">pyCRAC</requirement>
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4 </requirements>
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5 <command interpreter="python">
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6 /usr/local/bin/pyExtractLinesFromGTF.py --gtf $addGTF.gtf --genes_file $g --attribute $attribute $v -o $out
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7 </command>
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8 <version_command>/usr/local/bin/pyExtractLinesFromGTF.py --version</version_command>
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9 <inputs>
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10 <conditional name="addGTF">
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11 <param name="gtfFile" type="select" label="Choose GTF File from">
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12 <option value="default" selected="true">Defaults</option>
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13 <option value="other">History</option>
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14 </param>
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15 <when value="default">
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16 <param name="gtf" type="select" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates">
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17 <options from_data_table="pycrac_gtf"/>
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18 </param>
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19 </when>
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20 <when value="other">
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21 <param format="GTF" name="gtf" type="data" label="GTF File --gtf" help="GTF file containing gene ID co-ordinates"/>
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22 </when>
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23 </conditional>
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24 <param format="txt" name="g" type="data" label="File containing gene list --genes_file" help="Tabular file with 1 column of gene or annotation names"/>
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25 <param name="attribute" type="select" label="Select the attribute to extract names from --attribute">
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26 <option value="gene_name" selected="true">gene_name</option>
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27 <option value="gene_id">gene_id</option>
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28 <option value="transcript_name">transcript_name</option>
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29 <option value="transcript_id">transcript_id</option>
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30 </param>
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31 <param name="v" type="select" label="Extract lines from GTF that -v">
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32 <option value="" selected="true">Match the gene file</option>
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33 <option value="-v">Do not match in gene fil</option>
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34 </param>
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35 <param name="label" type="text" format="txt" size="30" value="pyExtractLinesFromGTF" label="Enter output file label -o" />
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36 </inputs>
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37
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38 <outputs>
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39 <data format="gtf" name="out" label="${label.value}.gtf"/>
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40 </outputs>
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41 <help>
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42 .. class:: infomark
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43
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44 **pyExtractLinesFromGTF**
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45
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46 pyExtractLinesFromGTF is part of the pyCRAC_ package. Extracts lines from a GTF file that contain gene names of interest.
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47
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48
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49 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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50
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51 ------
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52
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53 **Parameter list**
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54
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55 Options::
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56
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57 --gtf=Yourfavoritegtf.gtf
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58 type the path to the gtf file that you want to use. By
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59 default it expects data from the standard input.
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60 -g FILE, --genes_file=FILE
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61 name of your gene list or annotations list file (1
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62 column)
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63 -o OUTFILE, --outfile=OUTFILE
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64 type the name and path of the file you want to write
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65 the output to. Default is standard output
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66 -a ATTRIBUTE, --attribute=ATTRIBUTE
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67 from which attribute do you want to extract names?
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68 Choices: gene_name, gene_id, transcript_name,
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69 transcript_id
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70 -v
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71 similar to grep -v option. Remove the genes from the
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72 GTF that are in the gene list
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73
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74
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75
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76 </help>
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77 </tool>
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