comparison smart_toolShed/SMART/galaxy/plot.xml @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 <tool id="plot" name="Plot">
2 <description>Plot some information from a list of transcripts.</description>
3 <command interpreter="python">
4 ../Java/Python/plot.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'gff':
6 -f gff
7 #elif $formatType.FormatInputFileName == 'gff2':
8 -f gff2
9 #elif $formatType.FormatInputFileName == 'gff3':
10 -f gff3
11 #end if
12
13 -x $xLabel
14
15 -y $yLabel
16
17 -X $XVal
18 -Y $YVal
19
20 #if $optionLog.log == 'Yes' :
21 -l $optionLog.logOnAxisLabel
22 #end if
23
24 -s $shape
25 -o $outputFile
26
27 </command>
28
29 <inputs>
30 <conditional name="formatType">
31 <param name="FormatInputFileName" type="select" label="Input File Format">
32 <option value="gff">gff</option>
33 <option value="gff2">gff2</option>
34 <option value="gff3">gff3</option>
35 </param>
36 <when value="gff">
37 <param name="inputFileName" format="gff" type="data" label="Input File"/>
38 </when>
39 <when value="gff2">
40 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
41 </when>
42 <when value="gff3">
43 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
44 </when>
45 </conditional>
46
47 <param name="xLabel" type="text" value="value1" label="x label option" help="Choose one of the tags of 9th column in GFF file to be plotted as X-axis. Warning: You can only choose the tag value is digital."/>
48 <param name="yLabel" type="text" value="value2" label="y label option" help="Choose one of the tags of 9th column in GFF file to be plotted as Y-axis. You can only choose the tag value is digital."/>
49 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/>
50
51 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/>
52
53
54 <conditional name="optionLog">
55 <param name="log" type="select" label="calculate log option" help="use log on x- or y-axis (write 'x', 'y' or 'xy')">
56 <option value="Yes">Yes</option>
57 <option value="No" selected="true">No</option>
58 </param>
59 <when value="Yes">
60 <param name="logOnAxisLabel" type="text" value="y" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"/>
61 </when>
62 <when value="No">
63 </when>
64 </conditional>
65 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
66 </inputs>
67
68 <outputs>
69 <data name="outputFile" format="png" label="[plot] Output file"/>
70 </outputs>
71 </tool>