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comparison pyCRAC/pyGTF2bed.xml @ 0:19b20927172d draft

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author swebb
date Tue, 18 Jun 2013 09:11:00 -0400
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1 <tool id="pyGTF2bed" name="pyGTF2bed">
2 <description>converter</description>
3 <requirements>
4 <requirement type="package">pyCRAC</requirement>
5 </requirements>
6 <command interpreter="python">/usr/local/bin/pyGTF2bed.py --gtf $input -o $output
7 #if $addtrack.track == "--track":
8 --track
9 --name $addtrack.name
10 --description $addtrack.description
11 #if $addtrack.colorscheme.colorsel == "default":
12 -c $addtrack.colorscheme.color
13 #else:
14 -s '$addtrack.colorscheme.plus,$addtrack.colorscheme.minus'
15 #end if#
16 #end if#
17 </command>
18 <version_command>/usr/local/bin/pyGTF2bed.py --version</version_command>
19 <inputs>
20 <param name="input" type="data" format="gtf" label="GTF file --gtf"/>
21 <conditional name="addtrack">
22 <param name="track" type="select" label="Add UCSC track line to output --track">
23 <option value="" selected="true">NO</option>
24 <option value="--track">YES</option>
25 </param>
26 <when value=""/>
27 <when value="--track">
28 <param name="name" format="txt" type="text" value="User_supplied_track" size="80" label="Track name -n"/>
29 <param name="description" format="txt" type="text" value="User_supplied_track" size="80" label="Track description -d"/>
30 <conditional name="colorscheme">
31 <param name="colorsel" type="select" label="Colouring scheme">
32 <option value="default" selected="true">One Colour</option>
33 <option value="strand">By Strand</option>
34 </param>
35 <when value="default">
36 <param name="color" type="select" label="Choose track colour -c">
37 <option value="black" selected="true">Black</option>
38 <option value="red">Red</option>
39 <option value="blue">Blue</option>
40 <option value="green">Green</option>
41 <option value="purple">Purple</option>
42 </param>
43 </when>
44 <when value="strand">
45 <param name="plus" type="select" label="Choose forward strand track colour -s">
46 <option value="black" selected="true">Black</option>
47 <option value="red">Red</option>
48 <option value="blue">Blue</option>
49 <option value="green">Green</option>
50 <option value="purple">Purple</option>
51 </param>
52 <param name="minus" type="select" label="Choose minus strand track colour -s">
53 <option value="black" selected="true">Black</option>
54 <option value="red">Red</option>
55 <option value="blue">Blue</option>
56 <option value="green">Green</option>
57 <option value="purple">Purple</option>
58 </param>
59 </when>
60 </conditional>
61 </when>
62 </conditional>
63 <param name="label" type="text" format="txt" size="30" value="pyGTF2bed" label="Enter output file label -o" />
64 </inputs>
65 <outputs>
66 <data name="output" format="bed6" label="${label.value}.bed"/>
67 </outputs>
68 <help>
69
70 .. class:: infomark
71
72 **pyGTF2bed**
73
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.
75
76
77 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
78
79 ------
80
81 **Parameter list**
82
83 These options can be used to add and modify a track line for the UCSC genome browser::
84
85 --track
86 Use this flag to add a UCSC genome browser track line
87 to the beginning of your file
88 -n NAME, --name=NAME
89 For the USCS track line: provide a track name. Default
90 = 'User_supplied_track'
91 -d DESCRIPTION, --description=DESCRIPTION
92 For the USCS track line: provide a track description.
93 Default = 'User_supplied_track'
94 -c COLOR, --color=COLOR
95 select the track color. Default = black
96 -s STRANDS, --colorstrands=STRANDS
97 select the colors for each strand. Default =
98 'red,blue'
99
100 File input options::
101
102 --gtf=Yourfavoritegtf.gtf
103 type the path to the gtf file that you want to
104 convert. Default is standard input
105 </help>
106 </tool>
107