annotate SMART/galaxy/plotTranscriptList.xml @ 53:47310c4fb725

Uploaded
author m-zytnicki
date Fri, 10 Jan 2014 08:57:02 -0500
parents 2c0c0a89fad7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
38
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
1 <tool id="plotTranscriptList" name="plot transcript list">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
2 <description>Plot some information from a list of transcripts. </description>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
3 <requirements>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
4 <requirement type="set_environment">PYTHONPATH</requirement>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
5 </requirements>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
6 <command interpreter="python">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
7 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
8 #if $formatType.FormatInputFileName == 'gff':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
9 -f gff
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
10 #elif $formatType.FormatInputFileName == 'gff2':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
11 -f gff2
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
12 #elif $formatType.FormatInputFileName == 'gff3':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
13 -f gff3
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
14 #elif $formatType.FormatInputFileName == 'gtf':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
15 -f gtf
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
16 #end if
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
17
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
18 -x $xVal
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
19 -y $yVal
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
20 #if $optionz.z == 'Yes':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
21 -z $optionz.zVal
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
22 #end if
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
23
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
24 -X $XVal
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
25 -Y $YVal
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
26 -Z $ZVal
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
27
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
28 #if $optionxLab.xLab == 'Yes':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
29 -n $optionxLab.labVal
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
30 #end if
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
31 #if $optionyLab.yLab == 'Yes':
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
32 -m $optionyLab.labVal
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
33 #end if
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
34
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
35 $log
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
36 -s $shape
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
37 -b $bucket
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
38
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
39 -o $outputFilePNG
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
40 </command>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
41
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
42 <inputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
43 <conditional name="formatType">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
44 <param name="FormatInputFileName" type="select" label="Input File Format">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
45 <option value="gff">gff</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
46 <option value="gff2">gff2</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
47 <option value="gff3">gff3</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
48 <option value="gtf">gtf</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
49 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
50 <when value="gff">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
51 <param name="inputFileName" format="gff" type="data" label="Input File"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
52 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
53 <when value="gff2">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
54 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
55 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
56 <when value="gff3">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
57 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
58 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
59 <when value="gtf">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
60 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
61 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
62 </conditional>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
63
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
64 <param name="xVal" type="text" value="None" label="tag for the x value"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
65 <param name="yVal" type="text" value="None" label="tag for the y value"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
66
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
67 <conditional name="optionz">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
68 <param name="z" type="select" label="tag for the z value ">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
69 <option value="Yes">Yes</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
70 <option value="No" selected="true">No</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
71 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
72 <when value="Yes">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
73 <param name="zVal" type="text" value="None"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
74 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
75 <when value="No">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
76 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
77 </conditional>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
78
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
79 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
80
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
81 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
82
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
83 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present (if applicable)"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
84
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
85 <conditional name="optionxLab">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
86 <param name="xLab" type="select" label="label on the x-axis ">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
87 <option value="Yes">Yes</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
88 <option value="No" selected="true">No</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
89 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
90 <when value="Yes">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
91 <param name="labVal" type="text" value=" "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
92 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
93 <when value="No">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
94 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
95 </conditional>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
96 <conditional name="optionyLab">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
97 <param name="yLab" type="select" label="label on the y-axis ">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
98 <option value="Yes">Yes</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
99 <option value="No" selected="true">No</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
100 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
101 <when value="Yes">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
102 <param name="labVal" type="text" value=" "/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
103 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
104 <when value="No">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
105 </when>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
106 </conditional>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
107
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
108 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
109 <option value="" selected="true">No</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
110 <option value="-l x">log on the x-axis</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
111 <option value="-l y">log on the y-axis</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
112 <option value="-l xy">log on the x- and y-axis</option>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
113 </param>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
114
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
115 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
116 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
117
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
118 </inputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
119
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
120 <outputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
121 <data name="outputFilePNG" format="png" label="[plot transcript list] output file"/>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
122 </outputs>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
123
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
124 <help>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
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.
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
126
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
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*.
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
128
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
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.
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
130
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
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.
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
132
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
133 If you use a cloud plot, you can compute the Spearman's rho to quantify a correlation between your two tag values.
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
134 </help>
2c0c0a89fad7 Uploaded
m-zytnicki
parents:
diff changeset
135 </tool>