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1 <tool id="pyGTF2bed" name="pyGTF2bed">
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2 <description>converter</description>
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3 <requirements>
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4 <requirement type="package">pyCRAC</requirement>
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5 </requirements>
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6 <command interpreter="python">/usr/local/bin/pyGTF2bed.py --gtf $input -o $output
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7 #if $addtrack.track == "--track":
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8 --track
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9 --name $addtrack.name
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10 --description $addtrack.description
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11 #if $addtrack.colorscheme.colorsel == "default":
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12 -c $addtrack.colorscheme.color
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13 #else:
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14 -s '$addtrack.colorscheme.plus,$addtrack.colorscheme.minus'
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15 #end if#
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16 #end if#
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17 </command>
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18 <version_command>/usr/local/bin/pyGTF2bed.py --version</version_command>
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19 <inputs>
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20 <param name="input" type="data" format="gtf" label="GTF file --gtf"/>
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21 <conditional name="addtrack">
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22 <param name="track" type="select" label="Add UCSC track line to output --track">
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23 <option value="" selected="true">NO</option>
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24 <option value="--track">YES</option>
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25 </param>
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26 <when value=""/>
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27 <when value="--track">
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28 <param name="name" format="txt" type="text" value="User_supplied_track" size="80" label="Track name -n"/>
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29 <param name="description" format="txt" type="text" value="User_supplied_track" size="80" label="Track description -d"/>
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30 <conditional name="colorscheme">
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31 <param name="colorsel" type="select" label="Colouring scheme">
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32 <option value="default" selected="true">One Colour</option>
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33 <option value="strand">By Strand</option>
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34 </param>
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35 <when value="default">
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36 <param name="color" type="select" label="Choose track colour -c">
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37 <option value="black" selected="true">Black</option>
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38 <option value="red">Red</option>
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39 <option value="blue">Blue</option>
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40 <option value="green">Green</option>
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41 <option value="purple">Purple</option>
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42 </param>
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43 </when>
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44 <when value="strand">
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45 <param name="plus" type="select" label="Choose forward strand track colour -s">
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46 <option value="black" selected="true">Black</option>
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47 <option value="red">Red</option>
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48 <option value="blue">Blue</option>
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49 <option value="green">Green</option>
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50 <option value="purple">Purple</option>
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51 </param>
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52 <param name="minus" type="select" label="Choose minus strand track colour -s">
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53 <option value="black" selected="true">Black</option>
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54 <option value="red">Red</option>
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55 <option value="blue">Blue</option>
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56 <option value="green">Green</option>
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57 <option value="purple">Purple</option>
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58 </param>
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59 </when>
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60 </conditional>
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61 </when>
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62 </conditional>
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63 <param name="label" type="text" format="txt" size="30" value="pyGTF2bed" label="Enter output file label -o" />
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64 </inputs>
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65 <outputs>
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66 <data name="output" format="bed6" label="${label.value}.bed"/>
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67 </outputs>
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68 <help>
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69
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70 .. class:: infomark
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71
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72 **pyGTF2bed**
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73
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74 pyGTF2bed is part of the pyCRAC_ package. Converts GTF files to the bed 6 format. Gene names present in the GTF file will be included in the bed file.
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75
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76
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77 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
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78
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79 ------
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80
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81 **Parameter list**
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82
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83 These options can be used to add and modify a track line for the UCSC genome browser::
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84
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85 --track
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86 Use this flag to add a UCSC genome browser track line
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87 to the beginning of your file
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88 -n NAME, --name=NAME
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89 For the USCS track line: provide a track name. Default
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90 = 'User_supplied_track'
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91 -d DESCRIPTION, --description=DESCRIPTION
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92 For the USCS track line: provide a track description.
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93 Default = 'User_supplied_track'
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94 -c COLOR, --color=COLOR
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95 select the track color. Default = black
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96 -s STRANDS, --colorstrands=STRANDS
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97 select the colors for each strand. Default =
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98 'red,blue'
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99
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100 File input options::
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101
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102 --gtf=Yourfavoritegtf.gtf
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103 type the path to the gtf file that you want to
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104 convert. Default is standard input
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105 </help>
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106 </tool>
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107
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