Mercurial > repos > artbio > ngsplot

annotate replot.xml.notworking @ 0:3ca58369469c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
author artbio
date Wed, 06 Dec 2017 19:01:53 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
1 <tool id="replot" name="replot">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
2 <command interpreter="perl">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
3 #if $outtype.outtype2 == "prof":
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
4 runreplot.pl $input_zipfile $outtype.outtype2 $output_filename
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
5 $outtype.WD
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
6 $outtype.HG
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
7 $outtype.SE
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
8 $outtype.H
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
9 $outtype.MW
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
10 $outtype.Y.Y2
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
11 $outtype.Y.Y3
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
12 $outtype.LEG
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
13 $outtype.BOX
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
14 $outtype.VLN
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
15 $outtype.XYL
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
16 $outtype.LWD
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
17 $outtype.FS
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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diff changeset
18 #else if $outtype.outtype2 == "heatmap":
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
19 runreplot.pl $input_zipfile $outtype.outtype2 $output_filename
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
20 $outtype.GO.GO2
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
21 $outtype.GO.KNC
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
22 $outtype.GO.MIT
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
23 $outtype.GO.NRS
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
24 $outtype.LOW
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
25 $outtype.RR
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
26 $outtype.FC
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
27 $outtype.CO
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
28 $outtype.CD
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
29 $outtype.FS
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
30 dummy
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
31 dummy
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
32 dummy
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
33 #end if:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
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34
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
35 </command>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
36
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
37 <!-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
38
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
39
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
40 <-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
41
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
42 <inputs>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
43 <param type="data" name="input_zipfile" multiple="false" label="Input zip file created by ngsplot"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
44
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
45 <conditional name="outtype">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
46 <param type="select" name="outtype2" label="Select figure type to replot">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
47 <option value="prof">Coverage Profile</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
48 <option value="heatmap">Heatmap</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
49 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
50
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
51 <when value="prof">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
52 <param type="text" name="WD" value="8" label="Image width in inches" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
53 <param type="text" name="HG" value="7" label="Image height in inches" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
54 <param type="select" name="SE" label="Standard error shading" >
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
55 <option value="1">Yes, include standard error shading</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
56 <option value="0">No, exclude standard error shading</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
57 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
58 <param type="text" name="H" value="0" label="Opacity of shaded area under each curve" help="Use 0 for no shading. Suggested value of between 0 and 0.5 will add a semi-transparent shade under each curve."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
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59 <param type="text" name="MW" value="1" label="Moving window width to smooth average profiles" help="The unit of the window size is a data point. In ngs.plot, the number of data points on the X-axis is 100. A moving window width of 10 means averaging over 10% of the entire X-axis."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
60 <conditional name="Y">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
61 <param type="select" name="Y2" label="Define Y-axis scale?" >
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
62 <option value="no">No, let program decide</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
63 <option value="yes">Yes</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
64 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
65 <when value="yes">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
66 <param type="text" name="Y3" value="0,100" label="Y-axis min_val,max_val" help="Enter minimum and maximum value separated by comma" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
67 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
68 <when value="no">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
69 <param type="hidden" name="Y3" value="na" label="test"/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
70 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
71 </conditional>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
72 <param type="select" name="LEG" label="Draw legend?" >
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
73 <option value="1">Yes</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
74 <option value="0">No</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
75 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
76 <param type="select" name="BOX" label="Draw box around plot?" >
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
77 <option value="1">Yes</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
78 <option value="0">No</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
79 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
80 <param type="select" name="VLN" label="Draw vertical lines?" >
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
81 <option value="1">Yes</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
82 <option value="0">No</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
83 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
84 <param type="select" name="XYL" label="Draw axis labels?" >
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
85 <option value="1">Yes</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
86 <option value="0">No</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
87 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
88 <param type="text" name="LWD" value="3" label="Line width" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
89 <param type="text" name="FS" value="12" label="Font size" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
90 <!-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
91 <-->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
92
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
93 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
94 <when value="heatmap">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
95 <conditional name="GO">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
96 <param type="select" name="GO2" label="Gene order algorithm" >
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
97 <option value="total">Overall enrichment of the 1st profile (default)</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
98 <option value="hc">Hierarchial clustering</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
99 <option value="max">Peak value of the 1st profile</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
100 <option value="prod">Product of all profiles on the same region</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
101 <option value="diff">Difference between 1st and 2nd profiles</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
102 <option value="km">K-means clustering.</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
103 <option value="none">No ranking algorithm applied, use order in gene list.</option>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
104 </param>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
105 <when value="km">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
106 <param type="text" name="KNC" value="5" label="K-means: Number of clusters" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
107 <param type="text" name="MIT" value="20" label="K-means: Number of iterations" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
108 <param type="text" name="NRS" value="30" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
109 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
110 <when value="total">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
111 <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
112 <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
113 <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
114 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
115 <when value="hc">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
116 <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
117 <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
118 <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
119 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
120 <when value="max">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
121 <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
122 <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
123 <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
124 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
125 <when value="prod">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
126 <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
127 <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
128 <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
129 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
130 <when value="diff">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
131 <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
132 <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
133 <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
134 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
135 <when value="none">
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
136 <param type="hidden" name="KNC" value="NA" label="K-means: Number of clusters" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
137 <param type="hidden" name="MIT" value="NA" label="K-means: Number of iterations" help=""/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
138 <param type="hidden" name="NRS" value="NA" label="K-means: Number of random starts" help="K-means is prone to local optima. Restarting it repeatedly may help to find a better solution."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
139 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
140 </conditional>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
141 <param type="text" name="LOW" value="10" label="Low count cutoff in rank-based normalization" help="This number is in raw read counts."/>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
142 <param type="text" name="RR" value="30" label="Reduce ratio" help="This controls the heatmap height. The smaller the value, the taller the heatmap." />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
143 <param type="text" name="FC" value="0.02" label="Flooding fraction" help="The default value of 0.02 means that the minimum value is truncated at 2% and the maximum value is truncated at 98%. A higher fraction results in plots that have higher brightness but are less dynamic." />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
144 <param type="text" name="CO" value="default" label="Color for heatmap" help="For non bam-pair plots, input a single color. For bam-pair plots, use color-tri format (neg_color:[neu_color]:pos_color). Hint: must use R colors, such as darkgreen, yellow and blue2. The neutral color is optional(default=black)." />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
145 <param type="text" name="CD" value="0.6" label="Color distribution for heatmap" help="Must be a positive number. Hint: lower values give more widely spaced colors at the negative end. In other words, they shift the neutral color to positive values. If set to 1, the neutral color represents 0(i.e. no bias). If set to >1, the neutral color represents a negative value." />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
146 <param type="text" name="FS" value="12" label="Font size" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
147 </when>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
148 </conditional>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
149 <!--
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
150 -->
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
151 </inputs>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
152
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
153 <help></help>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
154 <outputs>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
155 <data format="pdf" name="output_filename" />
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
156 </outputs>
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'
artbio
parents:
diff changeset
157 </tool>