Mercurial > repos > guru-ananda > karyotype_plot

comparison karyotype/karyotype_plot.xml @ 0:b1e0bf394aa9 draft

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Imported from capsule None
author devteam
date Thu, 22 Jan 2015 10:40:48 -0500
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1 <tool id="karyotype_Plot_1" name="Karyotype Plotting tool" version="1.0.0">
2 <description>for multiple series </description>
3 <command interpreter="bash">\$R_SCRIPT_PATH/r_wrapper.sh $script_file</command>
4
5 <inputs>
6 <param name="main" type="text" value="" size="30" label="Plot Title"/>
7 <param name="xlab" type="text" value="" size="30" label="Label for x axis"/>
8 <param name="ylab" type="text" value="" size="30" label="Label for y axis"/>
9 <param name="lty" type="select" label="Backbone Line Type">
10 <option value="1">Solid</option>
11 <option value="2">Dashed</option>
12 <option value="3">Dotted</option>
13 </param>
14 <param name="col" type="select" label="Backbone Line Color">
15 <option value="1">Black</option>
16 <option value="2">Red</option>
17 <option value="3">Green</option>
18 <option value="4">Blue</option>
19 <option value="5">Cyan</option>
20 <option value="6">Magenta</option>
21 <option value="7">Yellow</option>
22 <option value="8">Gray</option>
23 </param>
24 <param name="lwd" type="float" label="Backbone Line Width" value="1.0"/>
25
26 <conditional name="legend">
27 <param name="status" type="select" label="Include legend?">
28 <option value="yes" selected="true">Yes</option>
29 <option value="no">No</option>
30 </param>
31 <when value="yes">
32 <param name="leg_title" type="text" value="" size="30" label="Legend title"/>
33 <param name="leg_pos" type="select" label="Legend position">
34 <option value="top" selected="true">top</option>
35 <option value="topright">topright</option>
36 <option value="topleft">topleft</option>
37 <option value="bottom">bottom</option>
38 <option value="bottomright">bottomright</option>
39 <option value="bottomleft">bottomleft</option>
40 <option value="left">left</option>
41 <option value="right">right</option>
42 <option value="center">center</option>
43 </param>
44 </when>
45 <when value="no">
46 </when>
47 </conditional>
48
49 <repeat name="series" title="Series">
50 <param name="input" type="data" format="tabular" label="Dataset"/>
51 <param name="chrcolumn" type="data_column" data_ref="input" label="Chromosome Column"/>
52 <param name="startcolumn" type="data_column" data_ref="input" numerical="True" label="Start Column"/>
53 <param name="endcolumn" type="data_column" data_ref="input" numerical="True" label="End Column"/>
54 <param name="fpch" type="select" label="Point Type">
55 <option value="1">Circle (hollow)</option>
56 <option value="2">Triangle (hollow)</option>
57 <option value="3">Cross</option>
58 <option value="4">Diamond (hollow)</option>
59 <option value="15">Square (filled)</option>
60 <option value="16">Circle (filled)</option>
61 <option value="17">Triangle (filled)</option>
62 </param>
63 <param name="fcol" type="select" label="Point Color">
64 <option value="1">Black</option>
65 <option value="2">Red</option>
66 <option value="3">Green</option>
67 <option value="4">Blue</option>
68 <option value="5">Cyan</option>
69 <option value="6">Magenta</option>
70 <option value="7">Yellow</option>
71 <option value="8">Gray</option>
72 </param>
73 <param name="fcex" type="float" label="Point Scale" value="1.0"/>
74 <param name="leg_text" type="text" value="" size="30" label="Legend text" help="Will be printed only if Include Legend option is set to Yes"/>
75 </repeat>
76 </inputs>
77
78 <configfiles>
79 <configfile name="script_file">
80 ## Setup R error handling to go to stderr
81 options( show.error.messages=F,
82 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) },
83 warn = -1 )
84 ## Determine range of all series in the plot
85 library('gtools')
86 chrlist = c()
87 coordrange = c( NULL, NULL )
88 #for $i, $s in enumerate( $series )
89 s${i} = read.table( "${s.input.file_name}" )
90 chrlist = union( chrlist, as.character(unique(s${i}[,${s.chrcolumn}])) )
91 coordrange = range( coordrange, range(s${i}[,${s.startcolumn}]), range(s${i}[,${s.endcolumn}]) )
92 #end for
93 chrlist=mixedsort(chrlist)
94 coordrange_byChr=list()
95 length(coordrange_byChr) = length(chrlist)*2
96 dim(coordrange_byChr) = c(length(chrlist),2)
97 ci=1
98 for (chr in chrlist) {
99 #for $i, $s in enumerate( $series )
100 s${i} = read.table( "${s.input.file_name}" )
101 if (nrow(s${i}[s${i}[,${s.chrcolumn}]==chr,]) > 0) {
102 coordrange_byChr[ci,]=range(coordrange_byChr[ci,], s${i}[s${i}[,${s.chrcolumn}]==chr,c(${s.startcolumn},${s.endcolumn})])
103 }
104 #end for
105 ci=ci+1
106 }
107 ## Open output PDF file
108 pdf( "${out_file1}" )
109 ## Dummy plot for axis / labels
110 plot( NULL, type="n", xlim=c(1,length(chrlist)), ylim=coordrange, axes=F, main="${main}", xlab="${xlab}", ylab="${ylab}" )
111 box()
112 axis(1,at=1:length(chrlist),labels=chrlist,cex.axis=0.9, las=2)
113 axis(2,at=seq(coordrange[1],coordrange[2], length.out=10))
114 ## Plot backbone lines for each chr
115 ci=1
116 for (chr in chrlist) {
117 lines(c(ci,ci),coordrange_byChr[ci,],lty=${lty},col=${col},lwd=${lwd})
118 ci=ci+1
119 }
120
121 legend_text=c()
122 pchlist=c()
123 colorlist=c()
124 ## Plot each series
125 #for $i, $s in enumerate( $series )
126 chrs=as.character(s${i}[,${s.chrcolumn}])
127 xvals=sapply(chrs,function(x) which(chrlist==x))
128 points(xvals, s${i}[,${s.startcolumn}], pch=${s.fpch}, cex=${s.fcex}, col=${s.fcol} )
129 legend_text[${i}+1] = "${s.leg_text}"
130 pchlist[${i}+1] = ${s.fpch}
131 colorlist[${i}+1] = ${s.fcol}
132 #end for
133
134 #if $legend['status'] == "yes"
135 legend_title = "$legend.leg_title"
136 legend_pos = "$legend.leg_pos"
137 legend(legend_pos, title=legend_title, legend=legend_text, pch=pchlist, col=colorlist)
138 #end if
139
140 ## Close the PDF file
141 devname = dev.off()
142 </configfile>
143 </configfiles>
144
145 <outputs>
146 <data format="pdf" name="out_file1" />
147 </outputs>
148
149 <requirements>
150 <requirement type="set_environment">R_SCRIPT_PATH</requirement>
151 <requirement type="package" version="2.15.0">R</requirement>
152 </requirements>
153
154 <help>
155 .. class:: infomark
156
157 **What it does**
158
159 This tool allows you to paint genomic regions of interest on chromosomes arranged in a karyotype-like fashion. It also allows you to have multiple series in a plot, with each series corresponding to a different feature/dataset.
160
161 -----
162
163 .. class:: warningmark
164
165 Chromosome lengths (backbone line) are determined based on min and max co-ordinates (by chromosome) in start and end columns respectively. For the series, only the co-ordiantes in start column are used for plotting.
166
167 -----
168
169 **Example**
170
171 Below is an example of a two series karyotype plot:
172
173 .. image:: ./static/operation_icons/karyotype_output.png
174 :height: 540
175 :width: 540
176
177 </help>
178 </tool>