Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/plotTranscriptList.xml @ 15:440ceca58672
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author | m-zytnicki |
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date | Mon, 22 Apr 2013 11:08:07 -0400 |
parents | 769e306b7933 |
children | 94ab73e8a190 |
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14:c79b9ae3f65f | 15:440ceca58672 |
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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 <command interpreter="python"> | 3 <command interpreter="python"> |
4 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName | 4 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName |
5 #if $formatType.FormatInputFileName == 'bed': | 5 #if $formatType.FormatInputFileName == 'gff': |
6 -f bed | |
7 #elif $formatType.FormatInputFileName == 'gff': | |
8 -f gff | 6 -f gff |
9 #elif $formatType.FormatInputFileName == 'gff2': | 7 #elif $formatType.FormatInputFileName == 'gff2': |
10 -f gff2 | 8 -f gff2 |
11 #elif $formatType.FormatInputFileName == 'gff3': | 9 #elif $formatType.FormatInputFileName == 'gff3': |
12 -f gff3 | 10 -f gff3 |
13 #elif $formatType.FormatInputFileName == 'sam': | |
14 -f sam | |
15 #elif $formatType.FormatInputFileName == 'gtf': | 11 #elif $formatType.FormatInputFileName == 'gtf': |
16 -f gtf | 12 -f gtf |
17 #end if | 13 #end if |
18 | 14 |
19 -x $xVal | 15 -x $xVal |
31 #end if | 27 #end if |
32 #if $optionyLab.yLab == 'Yes': | 28 #if $optionyLab.yLab == 'Yes': |
33 -m $optionyLab.labVal | 29 -m $optionyLab.labVal |
34 #end if | 30 #end if |
35 | 31 |
36 #if $optionyLog.log == 'Yes': | 32 $optionLog.log |
37 -l $optionyLog.logVal | |
38 #end if | |
39 | |
40 -s $shape | 33 -s $shape |
41 -b $bucket | 34 -b $bucket |
42 | 35 |
43 -o $outputFilePNG | 36 -o $outputFilePNG |
44 </command> | 37 </command> |
45 | 38 |
46 <inputs> | 39 <inputs> |
47 <conditional name="formatType"> | 40 <conditional name="formatType"> |
48 <param name="FormatInputFileName" type="select" label="Input File Format"> | 41 <param name="FormatInputFileName" type="select" label="Input File Format"> |
49 <option value="bed">bed</option> | |
50 <option value="gff">gff</option> | 42 <option value="gff">gff</option> |
51 <option value="gff2">gff2</option> | 43 <option value="gff2">gff2</option> |
52 <option value="gff3">gff3</option> | 44 <option value="gff3">gff3</option> |
53 <option value="sam">sam</option> | |
54 <option value="gtf">gtf</option> | 45 <option value="gtf">gtf</option> |
55 </param> | 46 </param> |
56 <when value="bed"> | |
57 <param name="inputFileName" format="bed" type="data" label="Input File"/> | |
58 </when> | |
59 <when value="gff"> | 47 <when value="gff"> |
60 <param name="inputFileName" format="gff" type="data" label="Input File"/> | 48 <param name="inputFileName" format="gff" type="data" label="Input File"/> |
61 </when> | 49 </when> |
62 <when value="gff2"> | 50 <when value="gff2"> |
63 <param name="inputFileName" format="gff2" type="data" label="Input File"/> | 51 <param name="inputFileName" format="gff2" type="data" label="Input File"/> |
64 </when> | 52 </when> |
65 <when value="gff3"> | 53 <when value="gff3"> |
66 <param name="inputFileName" format="gff3" type="data" label="Input File"/> | 54 <param name="inputFileName" format="gff3" type="data" label="Input File"/> |
67 </when> | 55 </when> |
68 <when value="sam"> | |
69 <param name="inputFileName" format="sam" type="data" label="Input File"/> | |
70 </when> | |
71 <when value="gtf"> | 56 <when value="gtf"> |
72 <param name="inputFileName" format="gtf" type="data" label="Input File"/> | 57 <param name="inputFileName" format="gtf" type="data" label="Input File"/> |
73 </when> | 58 </when> |
74 </conditional> | 59 </conditional> |
75 | 60 |
76 <param name="xVal" type="text" value="None" label="tag for the x value [compulsory option]"/> | 61 <param name="xVal" type="text" value="None" label="tag for the x value"/> |
77 <param name="yVal" type="text" value="None" label="tag for the y value [compulsory option]"/> | 62 <param name="yVal" type="text" value="None" label="tag for the y value"/> |
78 | 63 |
79 <conditional name="optionz"> | 64 <conditional name="optionz"> |
80 <param name="z" type="select" label="tag for the z value "> | 65 <param name="z" type="select" label="tag for the z value "> |
81 <option value="Yes">Yes</option> | 66 <option value="Yes">Yes</option> |
82 <option value="No" selected="true">No</option> | 67 <option value="No" selected="true">No</option> |
90 | 75 |
91 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/> | 76 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/> |
92 | 77 |
93 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/> | 78 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/> |
94 | 79 |
95 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present"/> | 80 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present (if applicable)"/> |
96 | 81 |
97 <conditional name="optionxLab"> | 82 <conditional name="optionxLab"> |
98 <param name="xLab" type="select" label="label on the x-axis "> | 83 <param name="xLab" type="select" label="label on the x-axis "> |
99 <option value="Yes">Yes</option> | 84 <option value="Yes">Yes</option> |
100 <option value="No" selected="true">No</option> | 85 <option value="No" selected="true">No</option> |
115 </when> | 100 </when> |
116 <when value="No"> | 101 <when value="No"> |
117 </when> | 102 </when> |
118 </conditional> | 103 </conditional> |
119 | 104 |
120 <conditional name="optionyLog"> | 105 <conditional name="optionLog"> |
121 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"> | 106 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')"> |
122 <option value="Yes">Yes</option> | 107 <option value="" selected="true">No</option> |
123 <option value="No" selected="true">No</option> | 108 <option value="-l x">log on the x-axis</option> |
109 <option value="-l y">log on the y-axis</option> | |
110 <option value="-l xy">log on the x- and y-axis</option> | |
124 </param> | 111 </param> |
125 <when value="Yes"> | |
126 <param name="logVal" type="text" value=" "/> | |
127 </when> | |
128 <when value="No"> | |
129 </when> | |
130 </conditional> | 112 </conditional> |
131 | 113 |
132 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/> | 114 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/> |
133 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/> | 115 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/> |
134 | 116 |
136 | 118 |
137 <outputs> | 119 <outputs> |
138 <data name="outputFilePNG" format="png" label="[plotTranscriptList]out file"/> | 120 <data name="outputFilePNG" format="png" label="[plotTranscriptList]out file"/> |
139 </outputs> | 121 </outputs> |
140 | 122 |
123 <help> | |
124 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. | |
125 | |
126 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*. | |
127 | |
128 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. | |
129 | |
130 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. | |
131 | |
132 If you use a cloud plot, you can compute the Spearman's rho to quantify a correlation between your two tag values. | |
133 </help> | |
141 </tool> | 134 </tool> |