Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/plotTranscriptList.xml @ 15:440ceca58672

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Uploaded
author m-zytnicki
date Mon, 22 Apr 2013 11:08:07 -0400
parents 769e306b7933
children 94ab73e8a190
comparison
equal deleted inserted replaced
14:c79b9ae3f65f 15:440ceca58672
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>