Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/SMART/galaxy/plotTranscriptList.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 <tool id="plotTranscriptList" name="plot transcript list">
2 <description>Plot some information from a list of transcripts. </description>
3 <command interpreter="python">
4 ../Java/Python/plotTranscriptList.py -i $formatType.inputFileName
5 #if $formatType.FormatInputFileName == 'bed':
6 -f bed
7 #elif $formatType.FormatInputFileName == 'gff':
8 -f gff
9 #elif $formatType.FormatInputFileName == 'gff2':
10 -f gff2
11 #elif $formatType.FormatInputFileName == 'gff3':
12 -f gff3
13 #elif $formatType.FormatInputFileName == 'sam':
14 -f sam
15 #elif $formatType.FormatInputFileName == 'gtf':
16 -f gtf
17 #end if
18
19 -x $xVal
20 -y $yVal
21 #if $optionz.z == 'Yes':
22 -z $optionz.zVal
23 #end if
24
25 -X $XVal
26 -Y $YVal
27 -Z $ZVal
28
29 #if $optionxLab.xLab == 'Yes':
30 -n $optionxLab.labVal
31 #end if
32 #if $optionyLab.yLab == 'Yes':
33 -m $optionyLab.labVal
34 #end if
35
36 #if $optionyLog.log == 'Yes':
37 -l $optionyLog.logVal
38 #end if
39
40 -s $shape
41 -b $bucket
42
43 -o $outputFilePNG
44 </command>
45
46 <inputs>
47 <conditional name="formatType">
48 <param name="FormatInputFileName" type="select" label="Input File Format">
49 <option value="bed">bed</option>
50 <option value="gff">gff</option>
51 <option value="gff2">gff2</option>
52 <option value="gff3">gff3</option>
53 <option value="sam">sam</option>
54 <option value="gtf">gtf</option>
55 </param>
56 <when value="bed">
57 <param name="inputFileName" format="bed" type="data" label="Input File"/>
58 </when>
59 <when value="gff">
60 <param name="inputFileName" format="gff" type="data" label="Input File"/>
61 </when>
62 <when value="gff2">
63 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
64 </when>
65 <when value="gff3">
66 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
67 </when>
68 <when value="sam">
69 <param name="inputFileName" format="sam" type="data" label="Input File"/>
70 </when>
71 <when value="gtf">
72 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
73 </when>
74 </conditional>
75
76 <param name="xVal" type="text" value="None" label="tag for the x value [compulsory option]"/>
77 <param name="yVal" type="text" value="None" label="tag for the y value [compulsory option]"/>
78
79 <conditional name="optionz">
80 <param name="z" type="select" label="tag for the z value ">
81 <option value="Yes">Yes</option>
82 <option value="No" selected="true">No</option>
83 </param>
84 <when value="Yes">
85 <param name="zVal" type="text" value="None"/>
86 </when>
87 <when value="No">
88 </when>
89 </conditional>
90
91 <param name="XVal" type="float" value="0.0" label="value for x when tag is not present "/>
92
93 <param name="YVal" type="float" value="0.0" label="value for y when tag is not present"/>
94
95 <param name="ZVal" type="float" value="0.0" label="value for z when tag is not present"/>
96
97 <conditional name="optionxLab">
98 <param name="xLab" type="select" label="label on the x-axis ">
99 <option value="Yes">Yes</option>
100 <option value="No" selected="true">No</option>
101 </param>
102 <when value="Yes">
103 <param name="labVal" type="text" value=" "/>
104 </when>
105 <when value="No">
106 </when>
107 </conditional>
108 <conditional name="optionyLab">
109 <param name="yLab" type="select" label="label on the y-axis ">
110 <option value="Yes">Yes</option>
111 <option value="No" selected="true">No</option>
112 </param>
113 <when value="Yes">
114 <param name="labVal" type="text" value=" "/>
115 </when>
116 <when value="No">
117 </when>
118 </conditional>
119
120 <conditional name="optionyLog">
121 <param name="log" type="select" label="use log on x- or y-axis (write 'x', 'y' or 'xy')">
122 <option value="Yes">Yes</option>
123 <option value="No" selected="true">No</option>
124 </param>
125 <when value="Yes">
126 <param name="logVal" type="text" value=" "/>
127 </when>
128 <when value="No">
129 </when>
130 </conditional>
131
132 <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)"/>
134
135 </inputs>
136
137 <outputs>
138 <data name="outputFilePNG" format="png" label="[plotTranscriptList]out file"/>
139 </outputs>
140
141 </tool>