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comparison SMART/galaxy/plotTranscriptList.xml @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
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30:5677346472b5 31:0ab839023fe4
1 <tool id="plotTranscriptList" name="plot transcript list"> 1 <tool id="plotTranscriptList" name="plot transcript list">
2 <description>Plot some information from a list of transcripts. </description> 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"> 3 <command interpreter="python">
7 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName 4 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName
8 #if $formatType.FormatInputFileName == 'gff': 5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff':
9 -f gff 8 -f gff
10 #elif $formatType.FormatInputFileName == 'gff2': 9 #elif $formatType.FormatInputFileName == 'gff2':
11 -f gff2 10 -f gff2
12 #elif $formatType.FormatInputFileName == 'gff3': 11 #elif $formatType.FormatInputFileName == 'gff3':
13 -f gff3 12 -f gff3
13 #elif $formatType.FormatInputFileName == 'sam':
14 -f sam
14 #elif $formatType.FormatInputFileName == 'gtf': 15 #elif $formatType.FormatInputFileName == 'gtf':
15 -f gtf 16 -f gtf
16 #end if 17 #end if
17 18
18 -x $xVal 19 -x $xVal
30 #end if 31 #end if
31 #if $optionyLab.yLab == 'Yes': 32 #if $optionyLab.yLab == 'Yes':
32 -m $optionyLab.labVal 33 -m $optionyLab.labVal
33 #end if 34 #end if
34 35
35 $log 36 #if $optionyLog.log == 'Yes':
37 -l $optionyLog.logVal
38 #end if
39
36 -s $shape 40 -s $shape
37 -b $bucket 41 -b $bucket
38 42
39 -o $outputFilePNG 43 -o $outputFilePNG
40 </command> 44 </command>
41 45
42 <inputs> 46 <inputs>
43 <conditional name="formatType"> 47 <conditional name="formatType">
44 <param name="FormatInputFileName" type="select" label="Input File Format"> 48 <param name="FormatInputFileName" type="select" label="Input File Format">
49 <option value="bed">bed</option>
45 <option value="gff">gff</option> 50 <option value="gff">gff</option>
46 <option value="gff2">gff2</option> 51 <option value="gff2">gff2</option>
47 <option value="gff3">gff3</option> 52 <option value="gff3">gff3</option>
53 <option value="sam">sam</option>
48 <option value="gtf">gtf</option> 54 <option value="gtf">gtf</option>
49 </param> 55 </param>
56 <when value="bed">
57 <param name="inputFileName" format="bed" type="data" label="Input File"/>
58 </when>
50 <when value="gff"> 59 <when value="gff">
51 <param name="inputFileName" format="gff" type="data" label="Input File"/> 60 <param name="inputFileName" format="gff" type="data" label="Input File"/>
52 </when> 61 </when>
53 <when value="gff2"> 62 <when value="gff2">
54 <param name="inputFileName" format="gff2" type="data" label="Input File"/> 63 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
55 </when> 64 </when>
56 <when value="gff3"> 65 <when value="gff3">
57 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 66 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
58 </when> 67 </when>
68 <when value="sam">
69 <param name="inputFileName" format="sam" type="data" label="Input File"/>
70 </when>
59 <when value="gtf"> 71 <when value="gtf">
60 <param name="inputFileName" format="gtf" type="data" label="Input File"/> 72 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
61 </when> 73 </when>
62 </conditional> 74 </conditional>
63 75
64 <param name="xVal" type="text" value="None" label="tag for the x value"/> 76 <param name="xVal" type="text" value="None" label="tag for the x value [compulsory option]"/>
65 <param name="yVal" type="text" value="None" label="tag for the y value"/> 77 <param name="yVal" type="text" value="None" label="tag for the y value [compulsory option]"/>
66 78
67 <conditional name="optionz"> 79 <conditional name="optionz">
68 <param name="z" type="select" label="tag for the z value "> 80 <param name="z" type="select" label="tag for the z value ">
69 <option value="Yes">Yes</option> 81 <option value="Yes">Yes</option>
70 <option value="No" selected="true">No</option> 82 <option value="No" selected="true">No</option>
78 90
79 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/> 91 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/>
80 92
81 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/> 93 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/>
82 94
83 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present (if applicable)"/> 95 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present"/>
84 96
85 <conditional name="optionxLab"> 97 <conditional name="optionxLab">
86 <param name="xLab" type="select" label="label on the x-axis "> 98 <param name="xLab" type="select" label="label on the x-axis ">
87 <option value="Yes">Yes</option> 99 <option value="Yes">Yes</option>
88 <option value="No" selected="true">No</option> 100 <option value="No" selected="true">No</option>
103 </when> 115 </when>
104 <when value="No"> 116 <when value="No">
105 </when> 117 </when>
106 </conditional> 118 </conditional>
107 119
108 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"> 120 <conditional name="optionyLog">
109 <option value="" selected="true">No</option> 121 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
110 <option value="-l x">log on the x-axis</option> 122 <option value="Yes">Yes</option>
111 <option value="-l y">log on the y-axis</option> 123 <option value="No" selected="true">No</option>
112 <option value="-l xy">log on the x- and y-axis</option> 124 </param>
113 </param> 125 <when value="Yes">
126 <param name="logVal" type="text" value=" "/>
127 </when>
128 <when value="No">
129 </when>
130 </conditional>
114 131
115 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/> 132 <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)"/> 133 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/>
117 134
118 </inputs> 135 </inputs>
119 136
120 <outputs> 137 <outputs>
121 <data name="outputFilePNG" format="png" label="[plot transcript list] output file"/> 138 <data name="outputFilePNG" format="png" label="[plotTranscriptList]out file"/>
122 </outputs> 139 </outputs>
123 140
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> 141 </tool>