Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/plotTranscriptList.xml @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
parents 440ceca58672
children 0ab839023fe4
comparison
equal deleted inserted replaced
17:b0e8584489e6 18:94ab73e8a190
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