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comparison pyCRAC/pyGTF2bedGraph.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="pyGTF2bedGraph" name="pyGTF2bedGraph">
2 <description>converter</description>
3 <requirements>
4 <requirement type="package">pyCRAC</requirement>
5 </requirements>
6 <command interpreter="perl">pyGTF2bedGraph.pl --gtf $input --po $po --mo $mo
7 --chromfile $addchr.chr
8 -t $type
9 --count $count
10 $iclip
11 #if $addtrack.track == "--track":
12 --track
13 --name $addtrack.name
14 --description $addtrack.description
15 #if $addtrack.colorscheme.colorsel == "default":
16 --color $addtrack.colorscheme.color
17 #else:
18 -s '$addtrack.colorscheme.plus,$addtrack.colorscheme.minus'
19 #end if#
20 #end if#
21 --id $po.id
22 </command>
23 <version_command>/usr/local/bin/pyGTF2bedGraph.py --version</version_command>
24 <inputs>
25 <param name="input" type="data" format="gtf" label="GTF file --gtf"/>
26 <conditional name="addchr">
27 <param name="chrfile" type="select" label="Choose Chromosome length file from">
28 <option value="default" selected="true">Defaults</option>
29 <option value="other">History</option>
30 </param>
31 <when value="default">
32 <param name="chr" type="select" label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes. Use pyCrac utility pyCalculateChromosomeLengths to create.">
33 <options from_data_table="pycrac_chr"/>
34 </param>
35 </when>
36 <when value="other">
37 <param format="tabular" name="chr" type="data" label="Chromosome length file -c" help="This file should have two columns: first column is the names of the chromosomes, second column is length of the chromosomes"/>
38 </when>
39 </conditional>
40 <param name="type" type="select" label="Choose type of data -t">
41 <option value="reads" selected="true">Reads</option>
42 <option value="substitutions">Substitutions</option>
43 <option value="deletions">Deletions</option>
44 </param>
45 <param format="integer" name="count" type="integer" label="Count per feature --count " value="1" size="5" help="Takes the numbers in the 'score' column of the GTF file as the total number of reads for each position" >
46 <validator type="in_range" min="1" message="Please enter a value >= 1"/>
47 </param>
48 <param name="iclip" type="select" label="iCLIP mode --iCLIP">
49 <option value="" selected="true">OFF</option>
50 <option value="--iCLIP">ON</option>
51 </param>
52 <conditional name="addtrack">
53 <param name="track" type="select" label="Add UCSC track line to output">
54 <option value="" selected="true">NO</option>
55 <option value="--track">YES</option>
56 </param>
57 <when value=""/>
58 <when value="--track">
59 <param name="name" format="txt" type="text" value="User_supplied_track" size="80" label="Track name"/>
60 <param name="description" format="txt" type="text" value="User_supplied_track" size="80" label="Track description"/>
61 <conditional name="colorscheme">
62 <param name="colorsel" type="select" label="Colouring scheme">
63 <option value="default" selected="true">One Colour</option>
64 <option value="strand">By Strand</option>
65 </param>
66 <when value="default">
67 <param name="color" type="select" label="Choose track colour">
68 <option value="black" selected="true">Black</option>
69 <option value="red">Red</option>
70 <option value="blue">Blue</option>
71 <option value="green">Green</option>
72 <option value="purple">Purple</option>
73 </param>
74 </when>
75 <when value="strand">
76 <param name="plus" type="select" label="Choose forward strand track colour">
77 <option value="black" selected="true">Black</option>
78 <option value="red">Red</option>
79 <option value="blue">Blue</option>
80 <option value="green">Green</option>
81 <option value="purple">Purple</option>
82 </param>
83 <param name="minus" type="select" label="Choose minus strand track colour">
84 <option value="black" selected="true">Black</option>
85 <option value="red">Red</option>
86 <option value="blue">Blue</option>
87 <option value="green">Green</option>
88 <option value="purple">Purple</option>
89 </param>
90 </when>
91 </conditional>
92 </when>
93 </conditional>
94 <param name="label" type="text" format="txt" size="30" value="pyGTF2bedGraph" label="Enter output file label -o" />
95 </inputs>
96 <outputs>
97 <data name="po" format="bedgraph" label="${label.value}_plus_strand.bg"/>
98 <data name="mo" format="bedgraph" label="${label.value}_minus_strand.bg"/>
99 </outputs>
100 <help>
101
102 .. class:: infomark
103
104 **pyGTF2bedGraph**
105
106 pyGTF2bedGraph is part of the pyCRAC_ package. Generates bedgraph files for each chromosome. An homage to bedtools genomecoverage. Takes a pyReadCounters GTF file as input file. Can also output bedGraph files for substitutions and deletions.
107
108 .. _pyCRAC: http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html
109
110 ------
111
112 **Parameter list**
113
114 File input options::
115
116 --gtf=readdata.gtf
117 type the path to the gtf file data file. Be default it
118 expects data from the standard input
119 -o converted
120 provide a name for an output file. A file extension or
121 strand information is not necessary.
122 -c yeast.txt, --chromfile=yeast.txt
123 Location of the chromosome info file. This file should
124 have two columns: first column is the names of the
125 chromosomes, second column is length of the
126 chromosomes. Default is yeast
127 -t TYPE, --type=TYPE
128 this tool can generate bedGraph files for reads,
129 substitutions or deletions. Please use
130 'reads','substitutions' or 'deletions' to indicate the
131 type of data. Default='reads'
132 --count
133 Takes the numbers in the 'score' column of the GTF
134 file as the total number of reads for each position.
135 Default is 1 for each interval.
136 --iCLIP
137 This turns on the iCLIP mode and the sgr reads or cDNA
138 files will report cross-linking site frequencies in
139 iCLIP data
140 -v, --verbose
141 to print status messages to a log file
142
143 These options can be used to add a track line for the UCSC genome browser::
144
145 --track
146 Use this flag to add a UCSC genome browser track line
147 to the beginning of your file
148 -n NAME, --name=NAME
149 For the USCS track line: provide a track name. Default
150 = 'User_supplied_track'
151 -d DESCRIPTION, --description=DESCRIPTION
152 For the USCS track line: provide a track description.
153 Default = 'User_supplied_track'
154 --color=COLOR
155 select the track color. Default = black
156 -s STRANDS, --colorstrands=STRANDS
157 select the colors for each strand. Default =
158 'red,blue'
159
160 </help>
161 </tool>
162