Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/plotTranscriptList.xml @ 38:2c0c0a89fad7
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author | m-zytnicki |
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date | Thu, 02 May 2013 09:56:47 -0400 |
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37:d22fadc825e3 | 38:2c0c0a89fad7 |
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1 <tool id="plotTranscriptList" name="plot transcript list"> | |
2 <description>Plot some information from a list of transcripts. </description> | |
3 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
6 <command interpreter="python"> | |
7 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName | |
8 #if $formatType.FormatInputFileName == 'gff': | |
9 -f gff | |
10 #elif $formatType.FormatInputFileName == 'gff2': | |
11 -f gff2 | |
12 #elif $formatType.FormatInputFileName == 'gff3': | |
13 -f gff3 | |
14 #elif $formatType.FormatInputFileName == 'gtf': | |
15 -f gtf | |
16 #end if | |
17 | |
18 -x $xVal | |
19 -y $yVal | |
20 #if $optionz.z == 'Yes': | |
21 -z $optionz.zVal | |
22 #end if | |
23 | |
24 -X $XVal | |
25 -Y $YVal | |
26 -Z $ZVal | |
27 | |
28 #if $optionxLab.xLab == 'Yes': | |
29 -n $optionxLab.labVal | |
30 #end if | |
31 #if $optionyLab.yLab == 'Yes': | |
32 -m $optionyLab.labVal | |
33 #end if | |
34 | |
35 $log | |
36 -s $shape | |
37 -b $bucket | |
38 | |
39 -o $outputFilePNG | |
40 </command> | |
41 | |
42 <inputs> | |
43 <conditional name="formatType"> | |
44 <param name="FormatInputFileName" type="select" label="Input File Format"> | |
45 <option value="gff">gff</option> | |
46 <option value="gff2">gff2</option> | |
47 <option value="gff3">gff3</option> | |
48 <option value="gtf">gtf</option> | |
49 </param> | |
50 <when value="gff"> | |
51 <param name="inputFileName" format="gff" type="data" label="Input File"/> | |
52 </when> | |
53 <when value="gff2"> | |
54 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | |
55 </when> | |
56 <when value="gff3"> | |
57 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | |
58 </when> | |
59 <when value="gtf"> | |
60 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | |
61 </when> | |
62 </conditional> | |
63 | |
64 <param name="xVal" type="text" value="None" label="tag for the x value"/> | |
65 <param name="yVal" type="text" value="None" label="tag for the y value"/> | |
66 | |
67 <conditional name="optionz"> | |
68 <param name="z" type="select" label="tag for the z value "> | |
69 <option value="Yes">Yes</option> | |
70 <option value="No" selected="true">No</option> | |
71 </param> | |
72 <when value="Yes"> | |
73 <param name="zVal" type="text" value="None"/> | |
74 </when> | |
75 <when value="No"> | |
76 </when> | |
77 </conditional> | |
78 | |
79 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/> | |
80 | |
81 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/> | |
82 | |
83 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present (if applicable)"/> | |
84 | |
85 <conditional name="optionxLab"> | |
86 <param name="xLab" type="select" label="label on the x-axis "> | |
87 <option value="Yes">Yes</option> | |
88 <option value="No" selected="true">No</option> | |
89 </param> | |
90 <when value="Yes"> | |
91 <param name="labVal" type="text" value=" "/> | |
92 </when> | |
93 <when value="No"> | |
94 </when> | |
95 </conditional> | |
96 <conditional name="optionyLab"> | |
97 <param name="yLab" type="select" label="label on the y-axis "> | |
98 <option value="Yes">Yes</option> | |
99 <option value="No" selected="true">No</option> | |
100 </param> | |
101 <when value="Yes"> | |
102 <param name="labVal" type="text" value=" "/> | |
103 </when> | |
104 <when value="No"> | |
105 </when> | |
106 </conditional> | |
107 | |
108 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"> | |
109 <option value="" selected="true">No</option> | |
110 <option value="-l x">log on the x-axis</option> | |
111 <option value="-l y">log on the y-axis</option> | |
112 <option value="-l xy">log on the x- and y-axis</option> | |
113 </param> | |
114 | |
115 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/> | |
116 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/> | |
117 | |
118 </inputs> | |
119 | |
120 <outputs> | |
121 <data name="outputFilePNG" format="png" label="[plot transcript list] output file"/> | |
122 </outputs> | |
123 | |
124 <help> | |
125 Plot the data attached as tags in a transcript list. This can be used for displaying the comparison of different sets of sliding windows, for instance. | |
126 | |
127 The tool reads the tags of a transcript file (actually, a GFF3 file). It considers more specifically the tag names that you specify as parameter. If you use only one tag name, you can display a line plot. In this case, you have to specify a bucket size *s* (which is by defaut 1) and a point (*x*, *y*) tells you that there are *y* transcripts with tag values *x* to *x + s*. | |
128 | |
129 You can display could plots if you use two tag names. Each point represents the values of the two tags of a transcript. If you use three variables, the third variable will be the color of the point. You can also use a log scale and name the axes of the plot. | |
130 | |
131 Each transcript must contain the tags which are specified. If not, you should provide a default value, which is used when the tag is not present. | |
132 | |
133 If you use a cloud plot, you can compute the Spearman's rho to quantify a correlation between your two tag values. | |
134 </help> | |
135 </tool> |