Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/plotTranscriptList.xml @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
parents | 440ceca58672 |
children | 0ab839023fe4 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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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 <requirements> | |
4 <requirement type="set_environment">PYTHONPATH</requirement> | |
5 </requirements> | |
3 <command interpreter="python"> | 6 <command interpreter="python"> |
4 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName | 7 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName |
5 #if $formatType.FormatInputFileName == 'gff': | 8 #if $formatType.FormatInputFileName == 'gff': |
6 -f gff | 9 -f gff |
7 #elif $formatType.FormatInputFileName == 'gff2': | 10 #elif $formatType.FormatInputFileName == 'gff2': |
27 #end if | 30 #end if |
28 #if $optionyLab.yLab == 'Yes': | 31 #if $optionyLab.yLab == 'Yes': |
29 -m $optionyLab.labVal | 32 -m $optionyLab.labVal |
30 #end if | 33 #end if |
31 | 34 |
32 $optionLog.log | 35 $log |
33 -s $shape | 36 -s $shape |
34 -b $bucket | 37 -b $bucket |
35 | 38 |
36 -o $outputFilePNG | 39 -o $outputFilePNG |
37 </command> | 40 </command> |
100 </when> | 103 </when> |
101 <when value="No"> | 104 <when value="No"> |
102 </when> | 105 </when> |
103 </conditional> | 106 </conditional> |
104 | 107 |
105 <conditional name="optionLog"> | 108 <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')"> | 109 <option value="" selected="true">No</option> |
107 <option value="" selected="true">No</option> | 110 <option value="-l x">log on the x-axis</option> |
108 <option value="-l x">log on the x-axis</option> | 111 <option value="-l y">log on the y-axis</option> |
109 <option value="-l y">log on the y-axis</option> | 112 <option value="-l xy">log on the x- and y-axis</option> |
110 <option value="-l xy">log on the x- and y-axis</option> | 113 </param> |
111 </param> | |
112 </conditional> | |
113 | 114 |
114 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/> | 115 <param name="shape" type="text" value="barplot" label="shape of the plot [format: choice (barplot, line, points, heatPoints)]"/> |
115 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/> | 116 <param name="bucket" type="float" value="1.0" label="bucket size (for the line plot)"/> |
116 | 117 |
117 </inputs> | 118 </inputs> |
118 | 119 |
119 <outputs> | 120 <outputs> |
120 <data name="outputFilePNG" format="png" label="[plotTranscriptList]out file"/> | 121 <data name="outputFilePNG" format="png" label="[plot transcript list] output file"/> |
121 </outputs> | 122 </outputs> |
122 | 123 |
123 <help> | 124 <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 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 |